Starting phenix.real_space_refine
on Thu Mar 13 21:41:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7na7_24267/03_2025/7na7_24267.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7na7_24267/03_2025/7na7_24267.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7na7_24267/03_2025/7na7_24267.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7na7_24267/03_2025/7na7_24267.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7na7_24267/03_2025/7na7_24267.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7na7_24267/03_2025/7na7_24267.cif"
  }
  resolution = 2.7
  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=   0.023
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    5786      2.51       5
     N    1526      2.21       5
     O    1662      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9036
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1752
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2584
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "G"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 418
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "N"
      Number of atoms: 1784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1784
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2339
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2339
          Classifications: {'peptide': 291}
          Link IDs: {'PTRANS': 11, 'TRANS': 279}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 103
          Classifications: {'peptide': 12}
          Link IDs: {'PTRANS': 1, 'TRANS': 10}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'1IC:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.45, per 1000 atoms: 0.71
  Number of scatterers: 9036
  At special positions: 0
  Unit cell: (87.75, 120.25, 124.8, 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    1662      8.00
     N    1526      7.00
     C    5786      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 159 " - pdb=" SG  CYS N 229 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 116 " - pdb=" SG  CYS R 198 " distance=2.03

  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: 2.10
  Conformation dependent library (CDL) restraints added in 961.3 milliseconds
  

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  1IC L   3 "
  Number of C-beta restraints generated:  2132

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 13 sheets defined
      38.0% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 32
      removed outlier: 3.587A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.359A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.519A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.017A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.699A  pdb=" N   GLU A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.697A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 328 through 352
    Processing helix  chain 'B' and resid 7 through 22
      removed outlier: 3.545A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ASN B  16 " --> pdb=" O   GLU B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 10 through 24
    Processing helix  chain 'G' and resid 30 through 44
      removed outlier: 4.444A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 40 through 71
      removed outlier: 4.142A  pdb=" N   ALA R  44 " --> pdb=" O   ALA R  40 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLY R  45 " --> pdb=" O   PRO R  41 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 72 through 75
    Processing helix  chain 'R' and resid 76 through 95
    Processing helix  chain 'R' and resid 95 through 105
    Processing helix  chain 'R' and resid 112 through 147
      removed outlier: 3.713A  pdb=" N   GLN R 120 " --> pdb=" O   CYS R 116 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   SER R 123 " --> pdb=" O   PHE R 119 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   TYR R 128 " --> pdb=" O   GLU R 124 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 147 through 155
      removed outlier: 3.607A  pdb=" N   VAL R 153 " --> pdb=" O   LEU R 149 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 157 through 176
      removed outlier: 3.570A  pdb=" N   LEU R 162 " --> pdb=" O   GLY R 158 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   VAL R 163 " --> pdb=" O   ARG R 159 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 182
    Processing helix  chain 'R' and resid 191 through 196
      removed outlier: 3.771A  pdb=" N   THR R 195 " --> pdb=" O   ASP R 191 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASN R 196 " --> pdb=" O   PRO R 192 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 191 through 196'
    Processing helix  chain 'R' and resid 202 through 207
    Processing helix  chain 'R' and resid 208 through 243
      removed outlier: 3.512A  pdb=" N   SER R 218 " --> pdb=" O   VAL R 214 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ILE R 219 " --> pdb=" O   TRP R 215 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   PHE R 220 " --> pdb=" O   VAL R 216 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   PHE R 221 " --> pdb=" O   SER R 217 " (cutoff:3.500A)
      Proline residue:  R 224  - end of helix
      removed outlier: 3.509A  pdb=" N   ARG R 243 " --> pdb=" O   LEU R 239 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 256 through 290
      Proline residue:  R 278  - end of helix
      removed outlier: 3.757A  pdb=" N   PHE R 290 " --> pdb=" O   PHE R 286 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 295 through 325
      removed outlier: 4.074A  pdb=" N   GLN R 299 " --> pdb=" O   LEU R 295 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLN R 302 " --> pdb=" O   ALA R 298 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA R 316 " --> pdb=" O   PHE R 312 " (cutoff:3.500A)
      Proline residue:  R 320  - end of helix
    Processing helix  chain 'R' and resid 327 through 338
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.172A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.545A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.544A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.518A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.733A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.057A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.765A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.659A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.649A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.010A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.802A  pdb=" N   MET N  34 " --> pdb=" O   TYR N  50 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   TYR N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12
      removed outlier: 4.223A  pdb=" N   PHE N 110 " --> pdb=" O   ARG N  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'N' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'N' and resid 146 through 148
      removed outlier: 6.345A  pdb=" N   LEU N 174 " --> pdb=" O   TYR N 190 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   TYR N 190 " --> pdb=" O   LEU N 174 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   TRP N 176 " --> pdb=" O   LEU N 188 " (cutoff:3.500A)

    442 hydrogen bonds defined for protein.
    1230 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: 2.70

  Time building geometry restraints manager: 2.49 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1446
        1.30 -     1.43: 2481
        1.43 -     1.56: 5218
        1.56 -     1.69: 0
        1.69 -     1.82: 88
  Bond restraints: 9233
  Sorted by residual:
  bond pdb=" CA  SER N 106 "
       pdb=" CB  SER N 106 "
    ideal  model  delta    sigma   weight residual
    1.531  1.449  0.082 1.22e-02 6.72e+03 4.51e+01
  bond pdb=" C   PRO N 107 "
       pdb=" O   PRO N 107 "
    ideal  model  delta    sigma   weight residual
    1.234  1.169  0.064 1.14e-02 7.69e+03 3.17e+01
  bond pdb=" CA  SER N 105 "
       pdb=" CB  SER N 105 "
    ideal  model  delta    sigma   weight residual
    1.529  1.447  0.082 1.61e-02 3.86e+03 2.62e+01
  bond pdb=" C   LEU N 174 "
       pdb=" O   LEU N 174 "
    ideal  model  delta    sigma   weight residual
    1.236  1.177  0.058 1.14e-02 7.69e+03 2.62e+01
  bond pdb=" C   TYR N 175 "
       pdb=" O   TYR N 175 "
    ideal  model  delta    sigma   weight residual
    1.234  1.185  0.048 1.17e-02 7.31e+03 1.71e+01
  ... (remaining 9228 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.26: 12259
        3.26 -     6.51: 225
        6.51 -     9.77: 19
        9.77 -    13.03: 2
       13.03 -    16.28: 2
  Bond angle restraints: 12507
  Sorted by residual:
  angle pdb=" C   1IC L   3 "
        pdb=" CA  1IC L   3 "
        pdb=" CB  1IC L   3 "
      ideal   model   delta    sigma   weight residual
     110.50  126.38  -15.88 1.50e+00 4.44e-01 1.12e+02
  angle pdb=" C   GLN R 302 "
        pdb=" CA  GLN R 302 "
        pdb=" CB  GLN R 302 "
      ideal   model   delta    sigma   weight residual
     110.63  126.91  -16.28 1.85e+00 2.92e-01 7.75e+01
  angle pdb=" N   GLU A   8 "
        pdb=" CA  GLU A   8 "
        pdb=" C   GLU A   8 "
      ideal   model   delta    sigma   weight residual
     112.92  103.28    9.64 1.23e+00 6.61e-01 6.14e+01
  angle pdb=" C   ARG N 191 "
        pdb=" CA  ARG N 191 "
        pdb=" CB  ARG N 191 "
      ideal   model   delta    sigma   weight residual
     111.80  122.64  -10.84 1.46e+00 4.69e-01 5.51e+01
  angle pdb=" N   LEU R 103 "
        pdb=" CA  LEU R 103 "
        pdb=" C   LEU R 103 "
      ideal   model   delta    sigma   weight residual
     113.01  105.72    7.29 1.20e+00 6.94e-01 3.69e+01
  ... (remaining 12502 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.69: 5470
       34.69 -    69.38: 85
       69.38 -   104.07: 7
      104.07 -   138.76: 3
      138.76 -   173.45: 4
  Dihedral angle restraints: 5569
    sinusoidal: 2266
      harmonic: 3303
  Sorted by residual:
  dihedral pdb=" C   GLN R 302 "
           pdb=" N   GLN R 302 "
           pdb=" CA  GLN R 302 "
           pdb=" CB  GLN R 302 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -141.66   19.06     0      2.50e+00 1.60e-01 5.81e+01
  dihedral pdb=" C   ARG N 191 "
           pdb=" N   ARG N 191 "
           pdb=" CA  ARG N 191 "
           pdb=" CB  ARG N 191 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.00   17.40     0      2.50e+00 1.60e-01 4.84e+01
  dihedral pdb=" C   ASN R 305 "
           pdb=" N   ASN R 305 "
           pdb=" CA  ASN R 305 "
           pdb=" CB  ASN R 305 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.94   15.34     0      2.50e+00 1.60e-01 3.76e+01
  ... (remaining 5566 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.166: 1416
       1.166 -    2.333: 0
       2.333 -    3.499: 0
       3.499 -    4.665: 0
       4.665 -    5.831: 2
  Chirality restraints: 1418
  Sorted by residual:
  chirality pdb=" C13 CLR R 402 "
            pdb=" C12 CLR R 402 "
            pdb=" C14 CLR R 402 "
            pdb=" C17 CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93    2.90   -5.83 2.00e-01 2.50e+01 8.50e+02
  chirality pdb=" C17 CLR R 402 "
            pdb=" C13 CLR R 402 "
            pdb=" C16 CLR R 402 "
            pdb=" C20 CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55   -2.63    5.18 2.00e-01 2.50e+01 6.72e+02
  chirality pdb=" CA  1IC L   3 "
            pdb=" N   1IC L   3 "
            pdb=" C   1IC L   3 "
            pdb=" CB  1IC L   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.84   -0.65 2.00e-01 2.50e+01 1.04e+01
  ... (remaining 1415 not shown)

  Planarity restraints: 1566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU N 174 "    0.026 2.00e-02 2.50e+03   5.27e-02 2.78e+01
        pdb=" C   LEU N 174 "   -0.091 2.00e-02 2.50e+03
        pdb=" O   LEU N 174 "    0.035 2.00e-02 2.50e+03
        pdb=" N   TYR N 175 "    0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A   6 "   -0.022 2.00e-02 2.50e+03   4.36e-02 1.90e+01
        pdb=" C   SER A   6 "    0.075 2.00e-02 2.50e+03
        pdb=" O   SER A   6 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ALA A   7 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL N 147 "   -0.047 5.00e-02 4.00e+02   7.10e-02 8.06e+00
        pdb=" N   PRO N 148 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO N 148 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO N 148 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1563 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 566
        2.72 -     3.27: 8743
        3.27 -     3.81: 14984
        3.81 -     4.36: 19413
        4.36 -     4.90: 33264
  Nonbonded interactions: 76970
  Sorted by model distance:
  nonbonded pdb=" OG1 THR R  76 "
            pdb=" OD1 ASN R  79 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" O   GLY R  57 "
            pdb=" ND2 ASN R  61 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" O   MET G  38 "
            pdb=" OE1 GLU G  42 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   PRO R 192 "
            pdb=" OD1 ASN R 196 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   PHE N  32 "
            pdb=" NH2 ARG N  72 "
     model   vdw
     2.322 3.120
  ... (remaining 76965 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=1.00 max=1.00 mean=1.00
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:             4.680
  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:          0.430
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.160
  Find NCS groups from input model:        0.120
  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:11.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
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   0.082   9233  Z= 0.402
  Angle     :  1.043  16.282  12507  Z= 0.655
  Chirality :  0.218   5.831   1418
  Planarity :  0.006   0.071   1566
  Dihedral  : 14.699 173.449   3428
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  3.98 %
    Favored  : 95.41 %
  Cbeta Deviations :  0.47 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.23), residues: 1119
  helix:  0.86 (0.26), residues: 388
  sheet:  0.67 (0.28), residues: 298
  loop : -0.62 (0.26), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP N 176 
 HIS   0.008   0.001   HIS B  54 
 PHE   0.019   0.002   PHE R 179 
 TYR   0.034   0.003   TYR N 102 
 ARG   0.009   0.001   ARG B 214 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 237
  time to evaluate  : 1.369 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.7165 (m-30) cc_final: 0.6770 (m-30)
REVERT: A  186 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6501 (mt-10)
REVERT: A  245 GLU cc_start: 0.6504 (tp30) cc_final: 0.6069 (tp30)
REVERT: A  316 THR cc_start: 0.8443 (m) cc_final: 0.8046 (p)
REVERT: B  137 ARG cc_start: 0.7770 (tpp-160) cc_final: 0.7519 (tpt90)
REVERT: N  150 THR cc_start: 0.8011 (t) cc_final: 0.7784 (p)
REVERT: R  237 ARG cc_start: 0.7084 (ttp80) cc_final: 0.6751 (ttp80)
REVERT: R  283 ARG cc_start: 0.6910 (mtp85) cc_final: 0.6671 (mtt-85)
REVERT: R  327 SER cc_start: 0.7871 (t) cc_final: 0.7481 (p)
REVERT: L   10 GLN cc_start: 0.5134 (mt0) cc_final: 0.4931 (pm20)
  outliers start: 6
  outliers final: 0
  residues processed: 241
  average time/residue: 1.2386
  time to fit residues: 320.4520
Evaluate side-chains
  205 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 57 optimal weight:    0.1980
   chunk 45 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9980
   chunk 33 optimal weight:    0.3980
   chunk 53 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 101 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  16 ASN
B 230 ASN
B 295 ASN
N  82 GLN
N 142 GLN
N 179 GLN
N 183 GLN
R 120 GLN
R 302 GLN
R 319 ASN
L   9 HIS
L  10 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.123707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.111309 restraints weight = 12685.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 1.49
r_work: 0.3371 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9233  Z= 0.235
  Angle     :  0.783  32.053  12507  Z= 0.365
  Chirality :  0.062   1.645   1418
  Planarity :  0.005   0.051   1566
  Dihedral  : 12.058 178.309   1375
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.35 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.24), residues: 1119
  helix:  1.21 (0.26), residues: 397
  sheet:  0.73 (0.28), residues: 295
  loop : -0.48 (0.28), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 169 
 HIS   0.006   0.001   HIS B 142 
 PHE   0.023   0.002   PHE A 189 
 TYR   0.022   0.001   TYR N 190 
 ARG   0.007   0.001   ARG A 208 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 214
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.7888 (m-30) cc_final: 0.7573 (m-30)
REVERT: A   29 LYS cc_start: 0.8240 (tttm) cc_final: 0.8008 (tttm)
REVERT: A  245 GLU cc_start: 0.7397 (tp30) cc_final: 0.7046 (tp30)
REVERT: A  316 THR cc_start: 0.8540 (m) cc_final: 0.8227 (p)
REVERT: A  345 LYS cc_start: 0.8549 (mttt) cc_final: 0.8288 (mttt)
REVERT: B  111 TYR cc_start: 0.8458 (m-80) cc_final: 0.8248 (m-80)
REVERT: B  137 ARG cc_start: 0.8211 (tpp-160) cc_final: 0.7874 (tpt90)
REVERT: N    4 LEU cc_start: 0.8476 (mt) cc_final: 0.8258 (mt)
REVERT: R  142 TYR cc_start: 0.8553 (t80) cc_final: 0.8284 (t80)
REVERT: R  150 ARG cc_start: 0.8187 (ttm110) cc_final: 0.7959 (ttm170)
REVERT: R  237 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7593 (ttp80)
REVERT: L   10 GLN cc_start: 0.6059 (mt0) cc_final: 0.5639 (pp30)
  outliers start: 22
  outliers final: 10
  residues processed: 222
  average time/residue: 1.2796
  time to fit residues: 303.5162
Evaluate side-chains
  213 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 203
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  158 SER
Chi-restraints excluded: chain N residue  184 SER
Chi-restraints excluded: chain R residue   73 GLU
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  307 VAL
Chi-restraints excluded: chain R residue  328 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0980
   chunk 92 optimal weight:    0.3980
   chunk 65 optimal weight:    0.9980
   chunk 103 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 175 GLN
B 295 ASN
G  17 GLN
N  82 GLN
N 179 GLN
** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   9 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.122478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.110211 restraints weight = 12875.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 1.49
r_work: 0.3355 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9233  Z= 0.218
  Angle     :  0.735  31.577  12507  Z= 0.336
  Chirality :  0.063   1.753   1418
  Planarity :  0.004   0.054   1566
  Dihedral  : 11.690 176.165   1375
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.49 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.24), residues: 1119
  helix:  1.42 (0.26), residues: 389
  sheet:  0.62 (0.29), residues: 286
  loop : -0.49 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.017   0.001   PHE A 189 
 TYR   0.016   0.001   TYR N 190 
 ARG   0.009   0.001   ARG R 283 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 219
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.7916 (m-30) cc_final: 0.7612 (m-30)
REVERT: A  243 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8024 (tpp)
REVERT: A  245 GLU cc_start: 0.7405 (tp30) cc_final: 0.7063 (tp30)
REVERT: A  316 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8281 (p)
REVERT: A  324 THR cc_start: 0.7518 (m) cc_final: 0.6863 (p)
REVERT: N    4 LEU cc_start: 0.8585 (mt) cc_final: 0.8287 (mt)
REVERT: N  192 MET cc_start: 0.8229 (ttp) cc_final: 0.7923 (ttp)
REVERT: R  142 TYR cc_start: 0.8548 (t80) cc_final: 0.8272 (t80)
REVERT: R  150 ARG cc_start: 0.8151 (ttm110) cc_final: 0.7932 (ttm170)
REVERT: R  237 ARG cc_start: 0.7921 (ttp80) cc_final: 0.7593 (ttp80)
REVERT: R  283 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7247 (mtt180)
REVERT: R  332 VAL cc_start: 0.8561 (p) cc_final: 0.8246 (m)
  outliers start: 29
  outliers final: 11
  residues processed: 232
  average time/residue: 1.1527
  time to fit residues: 285.6746
Evaluate side-chains
  219 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 205
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  184 SER
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  283 ARG
Chi-restraints excluded: chain R residue  307 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
B 239 ASN
B 295 ASN
N 179 GLN
R 186 HIS
R 302 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.120673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.108611 restraints weight = 12752.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.47
r_work: 0.3332 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.3402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   9233  Z= 0.320
  Angle     :  0.786  32.055  12507  Z= 0.360
  Chirality :  0.064   1.712   1418
  Planarity :  0.004   0.058   1566
  Dihedral  : 11.890 178.381   1375
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 15.39 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.24), residues: 1119
  helix:  1.26 (0.26), residues: 387
  sheet:  0.64 (0.28), residues: 294
  loop : -0.55 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 169 
 HIS   0.006   0.001   HIS B 142 
 PHE   0.018   0.002   PHE A 189 
 TYR   0.014   0.002   TYR R 313 
 ARG   0.007   0.001   ARG A  32 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 213
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.7943 (m-30) cc_final: 0.7642 (m-30)
REVERT: A  245 GLU cc_start: 0.7326 (tp30) cc_final: 0.7049 (tp30)
REVERT: B  150 ARG cc_start: 0.8833 (mmt-90) cc_final: 0.8616 (mpt180)
REVERT: B  258 ASP cc_start: 0.7878 (t0) cc_final: 0.7480 (t0)
REVERT: N  202 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.7693 (ttp-170)
REVERT: R  142 TYR cc_start: 0.8556 (t80) cc_final: 0.8326 (t80)
REVERT: R  150 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7893 (ttm170)
REVERT: R  237 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7581 (ttp80)
REVERT: R  283 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7081 (mtt180)
REVERT: R  332 VAL cc_start: 0.8561 (p) cc_final: 0.8273 (m)
  outliers start: 36
  outliers final: 21
  residues processed: 228
  average time/residue: 1.5312
  time to fit residues: 372.7531
Evaluate side-chains
  223 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 201
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  184 SER
Chi-restraints excluded: chain N residue  219 LEU
Chi-restraints excluded: chain R residue   69 SER
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  283 ARG
Chi-restraints excluded: chain R residue  300 ILE
Chi-restraints excluded: chain R residue  307 VAL
Chi-restraints excluded: chain R residue  328 LYS
Chi-restraints excluded: chain L residue   10 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 75 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B  17 GLN
B 156 GLN
B 239 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  82 GLN
N 179 GLN
R 186 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.122886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.110440 restraints weight = 12165.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.48
r_work: 0.3348 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.3653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9233  Z= 0.315
  Angle     :  0.774  30.932  12507  Z= 0.354
  Chirality :  0.064   1.747   1418
  Planarity :  0.004   0.061   1566
  Dihedral  : 11.781 174.698   1375
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 16.82 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.24), residues: 1119
  helix:  1.19 (0.26), residues: 388
  sheet:  0.54 (0.28), residues: 296
  loop : -0.56 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 169 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.018   0.002   PHE A 189 
 TYR   0.014   0.002   TYR R 313 
 ARG   0.007   0.000   ARG A  32 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 208
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.7979 (m-30) cc_final: 0.7646 (m-30)
REVERT: A  245 GLU cc_start: 0.7326 (tp30) cc_final: 0.7057 (tp30)
REVERT: A  260 THR cc_start: 0.8649 (m) cc_final: 0.8375 (p)
REVERT: A  324 THR cc_start: 0.7608 (m) cc_final: 0.7029 (p)
REVERT: B  258 ASP cc_start: 0.7883 (t0) cc_final: 0.7564 (t0)
REVERT: N    4 LEU cc_start: 0.8645 (mt) cc_final: 0.8426 (mt)
REVERT: N  140 MET cc_start: 0.8484 (mmm) cc_final: 0.8193 (mmt)
REVERT: N  223 ASP cc_start: 0.8301 (m-30) cc_final: 0.8002 (m-30)
REVERT: R   82 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8114 (mm)
REVERT: R  142 TYR cc_start: 0.8547 (t80) cc_final: 0.8305 (t80)
REVERT: R  237 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7546 (ttp80)
REVERT: R  270 PHE cc_start: 0.7589 (m-10) cc_final: 0.7343 (m-80)
REVERT: R  332 VAL cc_start: 0.8545 (p) cc_final: 0.8283 (m)
  outliers start: 36
  outliers final: 21
  residues processed: 225
  average time/residue: 1.3084
  time to fit residues: 315.7472
Evaluate side-chains
  229 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 207
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  184 SER
Chi-restraints excluded: chain N residue  219 LEU
Chi-restraints excluded: chain R residue   69 SER
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  300 ILE
Chi-restraints excluded: chain R residue  307 VAL
Chi-restraints excluded: chain R residue  328 LYS
Chi-restraints excluded: chain L residue   10 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   chunk 77 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 94 optimal weight:    1.9990
   chunk 103 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  44 GLN
B 156 GLN
B 239 ASN
B 295 ASN
N  82 GLN
N 179 GLN
R 186 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.121688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.109324 restraints weight = 12345.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.49
r_work: 0.3348 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9233  Z= 0.310
  Angle     :  0.774  30.799  12507  Z= 0.353
  Chirality :  0.064   1.756   1418
  Planarity :  0.004   0.062   1566
  Dihedral  : 11.752 174.745   1375
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 17.43 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.24), residues: 1119
  helix:  1.19 (0.26), residues: 388
  sheet:  0.54 (0.29), residues: 294
  loop : -0.57 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.018   0.002   PHE A 189 
 TYR   0.013   0.001   TYR R 313 
 ARG   0.011   0.001   ARG B  42 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 207
  time to evaluate  : 1.260 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8008 (m-30) cc_final: 0.7665 (m-30)
REVERT: A  243 MET cc_start: 0.8444 (tpp) cc_final: 0.8174 (tpp)
REVERT: A  245 GLU cc_start: 0.7310 (tp30) cc_final: 0.7024 (tp30)
REVERT: A  260 THR cc_start: 0.8653 (m) cc_final: 0.8386 (p)
REVERT: A  324 THR cc_start: 0.7635 (m) cc_final: 0.7043 (p)
REVERT: B   42 ARG cc_start: 0.7475 (mmm-85) cc_final: 0.7191 (mmm-85)
REVERT: B  150 ARG cc_start: 0.8860 (mmt-90) cc_final: 0.8641 (mpt180)
REVERT: B  258 ASP cc_start: 0.7870 (t0) cc_final: 0.7599 (t0)
REVERT: N  140 MET cc_start: 0.8500 (mmm) cc_final: 0.8221 (mmt)
REVERT: N  202 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8122 (ttp-170)
REVERT: R  142 TYR cc_start: 0.8533 (t80) cc_final: 0.8309 (t80)
REVERT: R  237 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7568 (ttp80)
REVERT: R  332 VAL cc_start: 0.8537 (p) cc_final: 0.8282 (m)
  outliers start: 37
  outliers final: 23
  residues processed: 224
  average time/residue: 1.2546
  time to fit residues: 300.4370
Evaluate side-chains
  230 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 206
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   23 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  184 SER
Chi-restraints excluded: chain N residue  202 ARG
Chi-restraints excluded: chain N residue  219 LEU
Chi-restraints excluded: chain R residue   69 SER
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  300 ILE
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain R residue  307 VAL
Chi-restraints excluded: chain R residue  328 LYS
Chi-restraints excluded: chain L residue   10 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 110 optimal weight:    0.7980
   chunk 44 optimal weight:    0.1980
   chunk 49 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 72 optimal weight:    0.2980
   chunk 78 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0370
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 156 GLN
B 239 ASN
N  82 GLN
N 179 GLN
R 186 HIS
L   9 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.123339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.110844 restraints weight = 12415.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 1.51
r_work: 0.3367 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.3852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9233  Z= 0.203
  Angle     :  0.740  30.739  12507  Z= 0.331
  Chirality :  0.063   1.764   1418
  Planarity :  0.004   0.061   1566
  Dihedral  : 11.667 175.071   1375
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 18.35 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.25), residues: 1119
  helix:  1.47 (0.27), residues: 381
  sheet:  0.41 (0.29), residues: 283
  loop : -0.48 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.015   0.001   PHE A 189 
 TYR   0.014   0.001   TYR N 190 
 ARG   0.010   0.000   ARG A  32 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 201
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8006 (m-30) cc_final: 0.7659 (m-30)
REVERT: A  243 MET cc_start: 0.8433 (tpp) cc_final: 0.8211 (tpp)
REVERT: A  245 GLU cc_start: 0.7295 (tp30) cc_final: 0.6991 (tp30)
REVERT: A  324 THR cc_start: 0.7514 (m) cc_final: 0.6923 (p)
REVERT: B   42 ARG cc_start: 0.7455 (mmm-85) cc_final: 0.7207 (mmm-85)
REVERT: B  150 ARG cc_start: 0.8851 (mmt-90) cc_final: 0.8622 (mpt180)
REVERT: B  215 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6738 (pp20)
REVERT: N  202 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8074 (ttp-170)
REVERT: R  124 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7186 (mm-30)
REVERT: R  142 TYR cc_start: 0.8521 (t80) cc_final: 0.8315 (t80)
REVERT: R  237 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7574 (ttp80)
REVERT: R  332 VAL cc_start: 0.8537 (p) cc_final: 0.8284 (m)
  outliers start: 28
  outliers final: 19
  residues processed: 213
  average time/residue: 1.2718
  time to fit residues: 289.0842
Evaluate side-chains
  217 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 196
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  202 ARG
Chi-restraints excluded: chain N residue  219 LEU
Chi-restraints excluded: chain R residue   69 SER
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  300 ILE
Chi-restraints excluded: chain R residue  328 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 108 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0370
   chunk 24 optimal weight:    0.0870
   chunk 105 optimal weight:    0.3980
   chunk 95 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.3836

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 156 GLN
B 239 ASN
N  82 GLN
N 179 GLN
R 186 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.124087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.111509 restraints weight = 12464.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.52
r_work: 0.3376 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.3924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9233  Z= 0.189
  Angle     :  0.729  30.737  12507  Z= 0.326
  Chirality :  0.063   1.765   1418
  Planarity :  0.004   0.061   1566
  Dihedral  : 11.647 175.867   1375
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 18.96 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.25), residues: 1119
  helix:  1.54 (0.27), residues: 379
  sheet:  0.27 (0.28), residues: 292
  loop : -0.40 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.016   0.001   PHE R 309 
 TYR   0.013   0.001   TYR N 190 
 ARG   0.010   0.000   ARG A  32 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 195
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8013 (m-30) cc_final: 0.7657 (m-30)
REVERT: A  197 LYS cc_start: 0.8275 (mtpm) cc_final: 0.7989 (mtpp)
REVERT: A  243 MET cc_start: 0.8446 (tpp) cc_final: 0.8221 (tpp)
REVERT: A  245 GLU cc_start: 0.7298 (tp30) cc_final: 0.7003 (tp30)
REVERT: A  324 THR cc_start: 0.7512 (m) cc_final: 0.6911 (p)
REVERT: N  202 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8068 (ttp-170)
REVERT: R  124 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7263 (mm-30)
REVERT: R  142 TYR cc_start: 0.8521 (t80) cc_final: 0.8316 (t80)
REVERT: R  237 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7586 (ttp80)
REVERT: R  270 PHE cc_start: 0.7607 (m-10) cc_final: 0.7344 (m-80)
REVERT: R  332 VAL cc_start: 0.8534 (p) cc_final: 0.8282 (m)
  outliers start: 27
  outliers final: 18
  residues processed: 206
  average time/residue: 1.1773
  time to fit residues: 259.0677
Evaluate side-chains
  215 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 196
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  202 ARG
Chi-restraints excluded: chain N residue  219 LEU
Chi-restraints excluded: chain R residue   69 SER
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  328 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 95 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0370
   chunk 110 optimal weight:    0.7980
   chunk 56 optimal weight:    0.3980
   chunk 111 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
B 156 GLN
B 239 ASN
B 293 ASN
N  82 GLN
N 179 GLN
R 186 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.124123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.111436 restraints weight = 12352.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 1.54
r_work: 0.3361 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.3970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9233  Z= 0.246
  Angle     :  0.755  30.739  12507  Z= 0.340
  Chirality :  0.064   1.765   1418
  Planarity :  0.004   0.065   1566
  Dihedral  : 11.719 176.274   1375
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 19.06 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.25), residues: 1119
  helix:  1.47 (0.27), residues: 379
  sheet:  0.32 (0.28), residues: 282
  loop : -0.44 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.016   0.002   PHE A 189 
 TYR   0.013   0.001   TYR R 313 
 ARG   0.012   0.001   ARG B  42 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 196
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.7993 (m-30) cc_final: 0.7638 (m-30)
REVERT: A  243 MET cc_start: 0.8434 (tpp) cc_final: 0.8159 (tpp)
REVERT: A  245 GLU cc_start: 0.7292 (tp30) cc_final: 0.7025 (tp30)
REVERT: A  324 THR cc_start: 0.7628 (m) cc_final: 0.7042 (p)
REVERT: B  215 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6559 (pp20)
REVERT: B  217 MET cc_start: 0.7906 (pmm) cc_final: 0.7450 (pmm)
REVERT: N  202 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8056 (ttp-170)
REVERT: R  142 TYR cc_start: 0.8528 (t80) cc_final: 0.8319 (t80)
REVERT: R  237 ARG cc_start: 0.7961 (ttp80) cc_final: 0.7546 (ttp80)
REVERT: R  332 VAL cc_start: 0.8537 (p) cc_final: 0.8285 (m)
  outliers start: 25
  outliers final: 19
  residues processed: 207
  average time/residue: 1.1258
  time to fit residues: 249.2986
Evaluate side-chains
  219 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 198
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  184 SER
Chi-restraints excluded: chain N residue  202 ARG
Chi-restraints excluded: chain N residue  219 LEU
Chi-restraints excluded: chain R residue   69 SER
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  328 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 98 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 45 optimal weight:    0.8980
   chunk 102 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 156 GLN
B 239 ASN
B 293 ASN
N  82 GLN
N 179 GLN
R 186 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.122581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.109984 restraints weight = 12408.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 1.51
r_work: 0.3357 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.4012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9233  Z= 0.270
  Angle     :  0.764  30.754  12507  Z= 0.345
  Chirality :  0.064   1.765   1418
  Planarity :  0.004   0.067   1566
  Dihedral  : 11.765 176.679   1375
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 19.78 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.25), residues: 1119
  helix:  1.45 (0.27), residues: 378
  sheet:  0.27 (0.28), residues: 283
  loop : -0.46 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.017   0.002   PHE A 189 
 TYR   0.013   0.001   TYR R 313 
 ARG   0.011   0.001   ARG A  32 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 196
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.7995 (m-30) cc_final: 0.7648 (m-30)
REVERT: A  197 LYS cc_start: 0.8271 (mtpm) cc_final: 0.8011 (mtpp)
REVERT: A  243 MET cc_start: 0.8428 (tpp) cc_final: 0.8150 (tpp)
REVERT: A  245 GLU cc_start: 0.7285 (tp30) cc_final: 0.7019 (tp30)
REVERT: A  324 THR cc_start: 0.7630 (m) cc_final: 0.7019 (p)
REVERT: B  215 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6665 (pp20)
REVERT: N  202 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8053 (ttp-170)
REVERT: R  142 TYR cc_start: 0.8530 (t80) cc_final: 0.8322 (t80)
REVERT: R  237 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7540 (ttp80)
REVERT: R  332 VAL cc_start: 0.8544 (p) cc_final: 0.8302 (m)
  outliers start: 23
  outliers final: 19
  residues processed: 207
  average time/residue: 1.1486
  time to fit residues: 254.8725
Evaluate side-chains
  218 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 197
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  184 SER
Chi-restraints excluded: chain N residue  202 ARG
Chi-restraints excluded: chain N residue  204 SER
Chi-restraints excluded: chain N residue  219 LEU
Chi-restraints excluded: chain R residue   69 SER
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  328 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 102 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0870
   chunk 37 optimal weight:    0.3980
   chunk 5 optimal weight:    3.9990
   chunk 96 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 156 GLN
B 239 ASN
B 293 ASN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 179 GLN
R 186 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.121632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.109294 restraints weight = 12767.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 1.49
r_work: 0.3336 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9233  Z= 0.239
  Angle     :  0.754  30.766  12507  Z= 0.339
  Chirality :  0.063   1.766   1418
  Planarity :  0.004   0.066   1566
  Dihedral  : 11.755 177.113   1375
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 19.88 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.25), residues: 1119
  helix:  1.45 (0.27), residues: 379
  sheet:  0.29 (0.29), residues: 282
  loop : -0.45 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.016   0.002   PHE A 189 
 TYR   0.012   0.001   TYR N 190 
 ARG   0.011   0.000   ARG A  32 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7866.77 seconds
wall clock time: 138 minutes 13.02 seconds (8293.02 seconds total)