Starting phenix.real_space_refine
on Mon May 19 04:23:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iru_35686/05_2025/8iru_35686_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iru_35686/05_2025/8iru_35686.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iru_35686/05_2025/8iru_35686.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iru_35686/05_2025/8iru_35686.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iru_35686/05_2025/8iru_35686_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iru_35686/05_2025/8iru_35686_neut_trim.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 5
    Type Number    sf(0)   Gaussians
     S      59      5.16       5
     C    5788      2.51       5
     N    1522      2.21       5
     O    1637      1.98       5
     H    8649      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 79 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 17655
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 3771
          Classifications: {'peptide': 231}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "B"
      Number of atoms: 5094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 5094
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
    Chain: "E"
      Number of atoms: 3492
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 3492
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 887
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "R"
      Number of atoms: 4137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 4137
          Classifications: {'peptide': 268}
          Link IDs: {'PTRANS': 14, 'TRANS': 253}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "R"
      Number of atoms: 274
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 274
          Unusual residues: {'CLR': 9, 'R5F': 1}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
  Time building chain proxies: 8.59, per 1000 atoms: 0.49
  Number of scatterers: 17655
  At special positions: 0
  Unit cell: (112.32, 132.84, 110.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      59     16.00
     O    1637      8.00
     N    1522      7.00
     C    5788      6.00
     H    8649      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 108 " - pdb=" SG  CYS R 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 372 " - pdb=" SG  CYS R 375 " distance=2.04

  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: 4.81
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2094

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 13 sheets defined
      39.8% alpha, 23.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.981A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
      removed outlier: 4.563A  pdb=" N   LYS A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 218
      removed outlier: 3.834A  pdb=" N   ASP A 217 " --> pdb=" O   CYS A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 245
    Processing helix  chain 'A' and resid 246 through 250
      removed outlier: 3.865A  pdb=" N   ARG A 250 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 270
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 298 through 320
      removed outlier: 3.799A  pdb=" N   ILE A 315 " --> pdb=" O   GLU A 311 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ALA A 318 " --> pdb=" O   ARG A 314 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   SER A 319 " --> pdb=" O   ILE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 358
    Processing helix  chain 'B' and resid 5 through 25
      removed outlier: 3.827A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 3.977A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 74 through 76
      No H-bonds generated for 'chain 'E' and resid 74 through 76'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.543A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 220 through 224
    Processing helix  chain 'G' and resid 10 through 24
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'R' and resid 33 through 62
    Processing helix  chain 'R' and resid 63 through 66
    Processing helix  chain 'R' and resid 69 through 87
      removed outlier: 4.278A  pdb=" N   ILE R  73 " --> pdb=" O   THR R  69 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 87 through 97
    Processing helix  chain 'R' and resid 104 through 139
      removed outlier: 3.553A  pdb=" N   VAL R 137 " --> pdb=" O   ARG R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 144
      removed outlier: 3.515A  pdb=" N   ASN R 144 " --> pdb=" O   PRO R 140 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 151 through 172
      Proline residue:  R 169  - end of helix
    Processing helix  chain 'R' and resid 173 through 177
      removed outlier: 3.801A  pdb=" N   VAL R 177 " --> pdb=" O   LEU R 174 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 189 through 201
    Processing helix  chain 'R' and resid 203 through 226
    Processing helix  chain 'R' and resid 343 through 372
      removed outlier: 3.758A  pdb=" N   LEU R 348 " --> pdb=" O   ALA R 344 " (cutoff:3.500A)
      Proline residue:  R 349  - end of helix
      Proline residue:  R 361  - end of helix
      removed outlier: 3.588A  pdb=" N   ALA R 370 " --> pdb=" O   HIS R 366 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 378 through 403
      removed outlier: 3.788A  pdb=" N   ASN R 392 " --> pdb=" O   LEU R 388 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   SER R 393 " --> pdb=" O   GLY R 389 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ALA R 394 " --> pdb=" O   TYR R 390 " (cutoff:3.500A)
      Proline residue:  R 397  - end of helix
      removed outlier: 4.514A  pdb=" N   PHE R 403 " --> pdb=" O   ILE R 399 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 404 through 412
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191
      removed outlier: 6.209A  pdb=" N   HIS A  34 " --> pdb=" O   HIS A 197 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   PHE A 199 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   LEU A  38 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ALA A 220 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.701A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   VAL B 327 " --> pdb=" O   TRP B 339 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.540A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.709A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.042A  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 153
      removed outlier: 3.658A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.524A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.455A  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: 6.697A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.549A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.764A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.361A  pdb=" N   VAL E 147 " --> pdb=" O   GLU E 246 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLY E 225 " --> pdb=" O   LEU E 245 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.361A  pdb=" N   VAL E 147 " --> pdb=" O   GLU E 246 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLY E 225 " --> pdb=" O   LEU E 245 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   THR E 238 " --> pdb=" O   GLN E 231 " (cutoff:3.500A)

    452 hydrogen bonds defined for protein.
    1263 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: 6.99

  Time building geometry restraints manager: 5.72 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 8623
        1.12 -     1.30: 1531
        1.30 -     1.47: 3451
        1.47 -     1.65: 4173
        1.65 -     1.82: 84
  Bond restraints: 17862
  Sorted by residual:
  bond pdb=" NH2 ARG R 346 "
       pdb="HH21 ARG R 346 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" CE1 PHE A 312 "
       pdb=" HE1 PHE A 312 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" CD2 PHE R 363 "
       pdb=" HD2 PHE R 363 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   ALA A  32 "
       pdb=" H   ALA A  32 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" NE  ARG A 205 "
       pdb=" HE  ARG A 205 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  ... (remaining 17857 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.74: 27570
        2.74 -     5.47: 3519
        5.47 -     8.21: 933
        8.21 -    10.95: 25
       10.95 -    13.69: 24
  Bond angle restraints: 32071
  Sorted by residual:
  angle pdb=" CA  PHE E  68 "
        pdb=" CB  PHE E  68 "
        pdb=" CG  PHE E  68 "
      ideal   model   delta    sigma   weight residual
     113.80  119.78   -5.98 1.00e+00 1.00e+00 3.58e+01
  angle pdb=" CA  ASP A 335 "
        pdb=" CB  ASP A 335 "
        pdb=" CG  ASP A 335 "
      ideal   model   delta    sigma   weight residual
     112.60  118.58   -5.98 1.00e+00 1.00e+00 3.58e+01
  angle pdb=" CA  ASN A  43 "
        pdb=" CB  ASN A  43 "
        pdb=" CG  ASN A  43 "
      ideal   model   delta    sigma   weight residual
     112.60  118.10   -5.50 1.00e+00 1.00e+00 3.02e+01
  angle pdb=" N   ILE A 275 "
        pdb=" CA  ILE A 275 "
        pdb=" C   ILE A 275 "
      ideal   model   delta    sigma   weight residual
     110.36  116.01   -5.65 1.05e+00 9.07e-01 2.90e+01
  angle pdb=" C   ASN B 119 "
        pdb=" N   ILE B 120 "
        pdb=" CA  ILE B 120 "
      ideal   model   delta    sigma   weight residual
     120.63  127.48   -6.85 1.33e+00 5.65e-01 2.65e+01
  ... (remaining 32066 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 8137
       17.92 -    35.84: 467
       35.84 -    53.77: 145
       53.77 -    71.69: 138
       71.69 -    89.61: 11
  Dihedral angle restraints: 8898
    sinusoidal: 5068
      harmonic: 3830
  Sorted by residual:
  dihedral pdb=" CA  LEU B 190 "
           pdb=" C   LEU B 190 "
           pdb=" N   SER B 191 "
           pdb=" CA  SER B 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.45   29.55     0      5.00e+00 4.00e-02 3.49e+01
  dihedral pdb=" CA  LEU B 284 "
           pdb=" C   LEU B 284 "
           pdb=" N   LEU B 285 "
           pdb=" CA  LEU B 285 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.82   29.18     0      5.00e+00 4.00e-02 3.40e+01
  dihedral pdb=" CA  TYR B 289 "
           pdb=" C   TYR B 289 "
           pdb=" N   ASP B 290 "
           pdb=" CA  ASP B 290 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.94   29.06     0      5.00e+00 4.00e-02 3.38e+01
  ... (remaining 8895 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 1032
       0.104 -    0.208: 360
       0.208 -    0.312: 44
       0.312 -    0.416: 6
       0.416 -    0.521: 1
  Chirality restraints: 1443
  Sorted by residual:
  chirality pdb=" CA  TYR B  59 "
            pdb=" N   TYR B  59 "
            pdb=" C   TYR B  59 "
            pdb=" CB  TYR B  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.52 2.00e-01 2.50e+01 6.77e+00
  chirality pdb=" CA  PHE R 202 "
            pdb=" N   PHE R 202 "
            pdb=" C   PHE R 202 "
            pdb=" CB  PHE R 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.18e+00
  chirality pdb=" CA  SER B 334 "
            pdb=" N   SER B 334 "
            pdb=" C   SER B 334 "
            pdb=" CB  SER B 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.88e+00
  ... (remaining 1440 not shown)

  Planarity restraints: 2625
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E  47 "    0.011 2.00e-02 2.50e+03   9.62e-02 3.70e+02
        pdb=" CG  TRP E  47 "   -0.092 2.00e-02 2.50e+03
        pdb=" CD1 TRP E  47 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD2 TRP E  47 "   -0.078 2.00e-02 2.50e+03
        pdb=" NE1 TRP E  47 "   -0.029 2.00e-02 2.50e+03
        pdb=" CE2 TRP E  47 "   -0.089 2.00e-02 2.50e+03
        pdb=" CE3 TRP E  47 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E  47 "   -0.078 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E  47 "    0.027 2.00e-02 2.50e+03
        pdb=" CH2 TRP E  47 "   -0.030 2.00e-02 2.50e+03
        pdb=" HD1 TRP E  47 "    0.032 2.00e-02 2.50e+03
        pdb=" HE1 TRP E  47 "    0.291 2.00e-02 2.50e+03
        pdb=" HE3 TRP E  47 "    0.048 2.00e-02 2.50e+03
        pdb=" HZ2 TRP E  47 "   -0.078 2.00e-02 2.50e+03
        pdb=" HZ3 TRP E  47 "    0.138 2.00e-02 2.50e+03
        pdb=" HH2 TRP E  47 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.257 2.00e-02 2.50e+03   1.06e-01 3.34e+02
        pdb=" CG  TYR B  59 "    0.102 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "    0.085 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "    0.114 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "    0.067 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "    0.043 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "    0.014 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "   -0.150 2.00e-02 2.50e+03
        pdb=" HD1 TYR B  59 "   -0.009 2.00e-02 2.50e+03
        pdb=" HD2 TYR B  59 "    0.055 2.00e-02 2.50e+03
        pdb=" HE1 TYR B  59 "    0.007 2.00e-02 2.50e+03
        pdb=" HE2 TYR B  59 "   -0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 222 "    0.158 2.00e-02 2.50e+03   9.05e-02 3.28e+02
        pdb=" CG  TRP R 222 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 222 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 222 "   -0.019 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 222 "   -0.050 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 222 "    0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 222 "   -0.062 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 222 "    0.056 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 222 "   -0.042 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 222 "    0.039 2.00e-02 2.50e+03
        pdb=" HD1 TRP R 222 "    0.035 2.00e-02 2.50e+03
        pdb=" HE1 TRP R 222 "   -0.231 2.00e-02 2.50e+03
        pdb=" HE3 TRP R 222 "   -0.098 2.00e-02 2.50e+03
        pdb=" HZ2 TRP R 222 "    0.119 2.00e-02 2.50e+03
        pdb=" HZ3 TRP R 222 "   -0.065 2.00e-02 2.50e+03
        pdb=" HH2 TRP R 222 "    0.089 2.00e-02 2.50e+03
  ... (remaining 2622 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 1130
        2.18 -     2.78: 31276
        2.78 -     3.39: 50402
        3.39 -     3.99: 68016
        3.99 -     4.60: 98479
  Nonbonded interactions: 249303
  Sorted by model distance:
  nonbonded pdb=" HG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     1.572 2.450
  nonbonded pdb=" HG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     1.581 2.450
  nonbonded pdb=" HH  TYR A 327 "
            pdb=" OD2 ASP A 348 "
     model   vdw
     1.581 2.450
  nonbonded pdb=" OD1 ASP R  80 "
            pdb=" HG  SER R 393 "
     model   vdw
     1.592 2.450
  nonbonded pdb=" OE1 GLU A  14 "
            pdb=" HG  SER E  52 "
     model   vdw
     1.593 2.450
  ... (remaining 249298 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:             0.320
  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:             0.310
  Extract box with map and model:          0.630
  Check model and map are aligned:         0.120
  Set scattering table:                    0.160
  Process input model:                     40.280
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
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      :  0.012   0.080   9217  Z= 0.734
  Angle     :  1.767  10.996  12556  Z= 1.174
  Chirality :  0.100   0.521   1443
  Planarity :  0.019   0.300   1549
  Dihedral  : 12.589  89.609   3813
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 0.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.48 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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: -0.54 (0.23), residues: 1107
  helix: -0.68 (0.23), residues: 382
  sheet:  0.53 (0.31), residues: 257
  loop : -0.41 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.093   0.022   TRP R 222 
 HIS   0.021   0.004   HIS B  54 
 PHE   0.076   0.014   PHE R 362 
 TYR   0.241   0.024   TYR B  59 
 ARG   0.017   0.001   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15149 (  449)
  hydrogen bonds       : angle       7.26712 ( 1263)
  SS BOND              : bond        0.00411 (    4)
  SS BOND              : angle       1.83877 (    8)
  covalent geometry    : bond        0.01221 ( 9213)
  covalent geometry    : angle       1.76692 (12548)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  333 is missing expected H atoms. Skipping.
Evaluate side-chains
  273 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 273
  time to evaluate  : 1.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 LYS cc_start: 0.8432 (mtpp) cc_final: 0.8206 (mttm)
REVERT: A  345 ASP cc_start: 0.8063 (m-30) cc_final: 0.7772 (m-30)
REVERT: A  357 ASP cc_start: 0.8083 (m-30) cc_final: 0.7399 (m-30)
REVERT: B  188 MET cc_start: 0.8786 (mmm) cc_final: 0.8541 (mmm)
REVERT: B  219 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7411 (mtt-85)
REVERT: B  279 SER cc_start: 0.8591 (p) cc_final: 0.8324 (p)
REVERT: G   18 GLN cc_start: 0.8260 (tp40) cc_final: 0.8024 (tp40)
REVERT: G   31 SER cc_start: 0.9041 (t) cc_final: 0.8794 (p)
REVERT: R  115 ASP cc_start: 0.8368 (t70) cc_final: 0.7985 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 273
  average time/residue: 0.5891
  time to fit residues: 208.8452
Evaluate side-chains
  175 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 83 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 86 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 64 optimal weight:    6.9990
   chunk 99 optimal weight:    5.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  28 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 ASN
R  33 GLN
R 175 ASN
R 369 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.110403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.084128 restraints weight = 47334.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 2.99
r_work: 0.3046 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.3485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9217  Z= 0.155
  Angle     :  0.641   7.617  12556  Z= 0.353
  Chirality :  0.043   0.155   1443
  Planarity :  0.005   0.044   1549
  Dihedral  :  7.418  58.414   1831
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  6.98 %
    Favored  : 92.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.37 (0.24), residues: 1107
  helix:  0.88 (0.25), residues: 396
  sheet:  0.25 (0.30), residues: 285
  loop : -0.20 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 222 
 HIS   0.006   0.001   HIS G  44 
 PHE   0.018   0.002   PHE R 362 
 TYR   0.021   0.002   TYR B 105 
 ARG   0.005   0.001   ARG A  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05003 (  449)
  hydrogen bonds       : angle       5.27669 ( 1263)
  SS BOND              : bond        0.00316 (    4)
  SS BOND              : angle       0.81557 (    8)
  covalent geometry    : bond        0.00327 ( 9213)
  covalent geometry    : angle       0.64118 (12548)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  333 is missing expected H atoms. Skipping.
Evaluate side-chains
  215 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 210
  time to evaluate  : 1.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8137 (mt-10)
REVERT: A  186 GLU cc_start: 0.8209 (tt0) cc_final: 0.7988 (tt0)
REVERT: A  281 GLU cc_start: 0.8655 (mp0) cc_final: 0.8111 (mp0)
REVERT: B   35 ASN cc_start: 0.8425 (m-40) cc_final: 0.8115 (m110)
REVERT: B   36 ASN cc_start: 0.9033 (m110) cc_final: 0.8721 (p0)
REVERT: B  118 ASP cc_start: 0.7988 (t0) cc_final: 0.7670 (p0)
REVERT: B  188 MET cc_start: 0.8830 (mmm) cc_final: 0.8554 (mmm)
REVERT: B  219 ARG cc_start: 0.8513 (ttm-80) cc_final: 0.8131 (mtt-85)
REVERT: E    3 GLN cc_start: 0.7996 (mp10) cc_final: 0.7733 (mp10)
REVERT: E  218 ARG cc_start: 0.8286 (ptp-110) cc_final: 0.7818 (mtm110)
REVERT: G   18 GLN cc_start: 0.8642 (tp40) cc_final: 0.8065 (tp-100)
REVERT: G   31 SER cc_start: 0.9474 (t) cc_final: 0.8820 (m)
REVERT: R  393 SER cc_start: 0.9420 (m) cc_final: 0.8673 (m)
  outliers start: 5
  outliers final: 3
  residues processed: 213
  average time/residue: 0.4550
  time to fit residues: 131.8172
Evaluate side-chains
  182 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 179
  time to evaluate  : 1.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain R residue  163 SER
Chi-restraints excluded: chain R residue  395 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 23 optimal weight:   10.0000
   chunk 97 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 90 optimal weight:    8.9990
   chunk 105 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 76 optimal weight:    9.9990
   chunk 81 optimal weight:    0.6980
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 ASN
B 293 ASN
R 392 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.108675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.082561 restraints weight = 47694.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 2.94
r_work: 0.3021 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.4111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9217  Z= 0.168
  Angle     :  0.575   7.369  12556  Z= 0.312
  Chirality :  0.040   0.150   1443
  Planarity :  0.004   0.040   1549
  Dihedral  :  6.704  59.857   1831
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 11.22 %
    Favored  : 88.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.25), residues: 1107
  helix:  1.47 (0.25), residues: 394
  sheet: -0.19 (0.31), residues: 269
  loop : -0.04 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 211 
 HIS   0.004   0.001   HIS B 266 
 PHE   0.013   0.002   PHE R 362 
 TYR   0.016   0.001   TYR B 105 
 ARG   0.003   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04187 (  449)
  hydrogen bonds       : angle       4.92510 ( 1263)
  SS BOND              : bond        0.00296 (    4)
  SS BOND              : angle       0.63481 (    8)
  covalent geometry    : bond        0.00364 ( 9213)
  covalent geometry    : angle       0.57457 (12548)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  333 is missing expected H atoms. Skipping.
Evaluate side-chains
  193 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 187
  time to evaluate  : 1.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 SER cc_start: 0.8798 (t) cc_final: 0.8039 (p)
REVERT: A  281 GLU cc_start: 0.8730 (mp0) cc_final: 0.8116 (mp0)
REVERT: B  118 ASP cc_start: 0.8094 (t0) cc_final: 0.7566 (p0)
REVERT: B  120 ILE cc_start: 0.9107 (mt) cc_final: 0.8907 (mp)
REVERT: B  188 MET cc_start: 0.8828 (mmm) cc_final: 0.8509 (mmm)
REVERT: B  219 ARG cc_start: 0.8641 (ttm-80) cc_final: 0.8255 (mtt-85)
REVERT: E    3 GLN cc_start: 0.8017 (mp10) cc_final: 0.7739 (mp10)
REVERT: G   18 GLN cc_start: 0.8606 (tp40) cc_final: 0.8380 (tp40)
REVERT: G   31 SER cc_start: 0.9475 (t) cc_final: 0.8973 (p)
REVERT: G   36 ASP cc_start: 0.8909 (m-30) cc_final: 0.8531 (m-30)
  outliers start: 6
  outliers final: 4
  residues processed: 191
  average time/residue: 0.4565
  time to fit residues: 120.0586
Evaluate side-chains
  175 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 171
  time to evaluate  : 1.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain R residue  130 SER
Chi-restraints excluded: chain R residue  197 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 57 optimal weight:    7.9990
   chunk 61 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   chunk 84 optimal weight:    9.9990
   chunk 50 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 32 optimal weight:    0.2980
   chunk 21 optimal weight:    2.9990
   chunk 99 optimal weight:    9.9990
   chunk 104 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.109270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.083788 restraints weight = 47460.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 2.90
r_work: 0.3041 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.4527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9217  Z= 0.133
  Angle     :  0.531   6.460  12556  Z= 0.286
  Chirality :  0.039   0.151   1443
  Planarity :  0.004   0.040   1549
  Dihedral  :  6.341  59.863   1831
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.85 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.88 (0.25), residues: 1107
  helix:  1.84 (0.26), residues: 389
  sheet: -0.11 (0.31), residues: 268
  loop :  0.03 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.011   0.001   PHE R 201 
 TYR   0.015   0.001   TYR B 105 
 ARG   0.003   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03735 (  449)
  hydrogen bonds       : angle       4.64874 ( 1263)
  SS BOND              : bond        0.00285 (    4)
  SS BOND              : angle       0.51336 (    8)
  covalent geometry    : bond        0.00286 ( 9213)
  covalent geometry    : angle       0.53096 (12548)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  333 is missing expected H atoms. Skipping.
Evaluate side-chains
  197 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 185
  time to evaluate  : 1.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 SER cc_start: 0.8812 (t) cc_final: 0.8121 (p)
REVERT: B   12 GLU cc_start: 0.9237 (tp30) cc_final: 0.9030 (mt-10)
REVERT: B  188 MET cc_start: 0.8773 (mmm) cc_final: 0.8479 (mmm)
REVERT: B  219 ARG cc_start: 0.8587 (ttm-80) cc_final: 0.8174 (mtt-85)
REVERT: E    3 GLN cc_start: 0.8022 (mp10) cc_final: 0.7736 (mp10)
REVERT: G   31 SER cc_start: 0.9463 (t) cc_final: 0.8990 (p)
REVERT: G   36 ASP cc_start: 0.9007 (m-30) cc_final: 0.8587 (m-30)
REVERT: R  390 TYR cc_start: 0.8722 (m-10) cc_final: 0.8476 (m-10)
  outliers start: 12
  outliers final: 10
  residues processed: 191
  average time/residue: 0.5199
  time to fit residues: 139.2669
Evaluate side-chains
  175 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 165
  time to evaluate  : 1.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   80 ASP
Chi-restraints excluded: chain R residue  130 SER
Chi-restraints excluded: chain R residue  197 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 39 optimal weight:    0.4980
   chunk 94 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 84 optimal weight:    9.9990
   chunk 100 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
** G  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  59 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.108348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.082303 restraints weight = 48491.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 2.95
r_work: 0.3022 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.4811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9217  Z= 0.161
  Angle     :  0.531   6.528  12556  Z= 0.287
  Chirality :  0.040   0.144   1443
  Planarity :  0.004   0.043   1549
  Dihedral  :  6.263  59.204   1831
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 13.02 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.91 (0.25), residues: 1107
  helix:  1.89 (0.26), residues: 388
  sheet: -0.19 (0.30), residues: 272
  loop :  0.10 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 211 
 HIS   0.006   0.001   HIS R 366 
 PHE   0.016   0.001   PHE E  68 
 TYR   0.015   0.001   TYR B 105 
 ARG   0.002   0.000   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03704 (  449)
  hydrogen bonds       : angle       4.58964 ( 1263)
  SS BOND              : bond        0.00275 (    4)
  SS BOND              : angle       0.52635 (    8)
  covalent geometry    : bond        0.00350 ( 9213)
  covalent geometry    : angle       0.53137 (12548)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  333 is missing expected H atoms. Skipping.
Evaluate side-chains
  190 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 175
  time to evaluate  : 1.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 SER cc_start: 0.8812 (t) cc_final: 0.8157 (p)
REVERT: B  217 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8201 (ptt)
REVERT: B  340 ASN cc_start: 0.7092 (OUTLIER) cc_final: 0.6684 (m110)
REVERT: E    3 GLN cc_start: 0.8009 (mp10) cc_final: 0.7740 (mp10)
REVERT: E   42 GLU cc_start: 0.8620 (pm20) cc_final: 0.8399 (pm20)
REVERT: E  220 GLU cc_start: 0.7466 (mp0) cc_final: 0.6785 (mp0)
REVERT: G   31 SER cc_start: 0.9477 (t) cc_final: 0.8993 (p)
REVERT: G   36 ASP cc_start: 0.9008 (m-30) cc_final: 0.8662 (m-30)
REVERT: R  390 TYR cc_start: 0.8549 (m-10) cc_final: 0.8332 (m-10)
  outliers start: 15
  outliers final: 12
  residues processed: 185
  average time/residue: 0.4222
  time to fit residues: 109.3677
Evaluate side-chains
  177 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 163
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain R residue   80 ASP
Chi-restraints excluded: chain R residue  130 SER
Chi-restraints excluded: chain R residue  163 SER
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  203 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 78 optimal weight:    8.9990
   chunk 25 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 109 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 103 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 88 optimal weight:    3.9990
   chunk 23 optimal weight:    8.9990
   chunk 93 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.105678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.079612 restraints weight = 48822.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 2.92
r_work: 0.2970 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.4926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   9217  Z= 0.285
  Angle     :  0.596   7.869  12556  Z= 0.324
  Chirality :  0.042   0.138   1443
  Planarity :  0.004   0.052   1549
  Dihedral  :  6.605  58.794   1831
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.02 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.62 (0.25), residues: 1107
  helix:  1.63 (0.26), residues: 394
  sheet: -0.41 (0.30), residues: 277
  loop :  0.00 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 339 
 HIS   0.007   0.002   HIS B  54 
 PHE   0.017   0.002   PHE R 201 
 TYR   0.018   0.002   TYR B 105 
 ARG   0.006   0.000   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03931 (  449)
  hydrogen bonds       : angle       4.76422 ( 1263)
  SS BOND              : bond        0.00331 (    4)
  SS BOND              : angle       0.79506 (    8)
  covalent geometry    : bond        0.00627 ( 9213)
  covalent geometry    : angle       0.59540 (12548)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  333 is missing expected H atoms. Skipping.
Evaluate side-chains
  184 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 164
  time to evaluate  : 1.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 SER cc_start: 0.8874 (t) cc_final: 0.8290 (p)
REVERT: B  118 ASP cc_start: 0.8113 (t0) cc_final: 0.7561 (p0)
REVERT: B  188 MET cc_start: 0.8915 (mmm) cc_final: 0.8585 (mmm)
REVERT: B  217 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8305 (ptt)
REVERT: E    3 GLN cc_start: 0.8071 (mp10) cc_final: 0.7808 (mp10)
REVERT: G   31 SER cc_start: 0.9492 (t) cc_final: 0.9011 (p)
REVERT: G   36 ASP cc_start: 0.8980 (m-30) cc_final: 0.8623 (m-30)
REVERT: R   80 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7677 (t70)
  outliers start: 20
  outliers final: 14
  residues processed: 175
  average time/residue: 0.4171
  time to fit residues: 103.4775
Evaluate side-chains
  174 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 158
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain G residue   15 LEU
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain R residue   45 ILE
Chi-restraints excluded: chain R residue   80 ASP
Chi-restraints excluded: chain R residue  130 SER
Chi-restraints excluded: chain R residue  163 SER
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  358 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 109 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   chunk 82 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 108 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 293 ASN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.108277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.082410 restraints weight = 48059.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.93
r_work: 0.3023 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.5059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9217  Z= 0.127
  Angle     :  0.515   6.393  12556  Z= 0.277
  Chirality :  0.040   0.150   1443
  Planarity :  0.003   0.033   1549
  Dihedral  :  6.154  55.265   1831
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 13.44 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.81 (0.25), residues: 1107
  helix:  1.90 (0.26), residues: 388
  sheet: -0.37 (0.31), residues: 275
  loop :  0.04 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 211 
 HIS   0.006   0.001   HIS R 366 
 PHE   0.012   0.001   PHE R 201 
 TYR   0.013   0.001   TYR B 105 
 ARG   0.002   0.000   ARG A  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03489 (  449)
  hydrogen bonds       : angle       4.51198 ( 1263)
  SS BOND              : bond        0.00271 (    4)
  SS BOND              : angle       0.43865 (    8)
  covalent geometry    : bond        0.00274 ( 9213)
  covalent geometry    : angle       0.51510 (12548)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  333 is missing expected H atoms. Skipping.
Evaluate side-chains
  184 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 170
  time to evaluate  : 1.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 SER cc_start: 0.8830 (t) cc_final: 0.8218 (p)
REVERT: B  118 ASP cc_start: 0.8180 (t0) cc_final: 0.7544 (p0)
REVERT: B  188 MET cc_start: 0.8751 (mmm) cc_final: 0.8382 (mmm)
REVERT: B  217 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8230 (ptt)
REVERT: E    3 GLN cc_start: 0.8036 (mp10) cc_final: 0.7772 (mp10)
REVERT: G   18 GLN cc_start: 0.8487 (tp40) cc_final: 0.8107 (tp40)
REVERT: G   31 SER cc_start: 0.9475 (t) cc_final: 0.9000 (p)
REVERT: G   36 ASP cc_start: 0.8979 (m-30) cc_final: 0.8638 (m-30)
  outliers start: 14
  outliers final: 13
  residues processed: 178
  average time/residue: 0.4396
  time to fit residues: 108.2975
Evaluate side-chains
  174 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 160
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain R residue   80 ASP
Chi-restraints excluded: chain R residue  163 SER
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  203 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0970
   chunk 96 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0870
   chunk 72 optimal weight:    0.5980
   chunk 80 optimal weight:    9.9990
   overall best weight:    0.5358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.110283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.084658 restraints weight = 47727.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 2.92
r_work: 0.3063 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.5273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9217  Z= 0.100
  Angle     :  0.496   5.611  12556  Z= 0.263
  Chirality :  0.039   0.149   1443
  Planarity :  0.003   0.042   1549
  Dihedral  :  5.876  55.585   1831
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 13.02 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.99 (0.25), residues: 1107
  helix:  2.11 (0.26), residues: 389
  sheet: -0.32 (0.30), residues: 273
  loop :  0.11 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 366 
 PHE   0.009   0.001   PHE R 201 
 TYR   0.014   0.001   TYR R 390 
 ARG   0.004   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03260 (  449)
  hydrogen bonds       : angle       4.32346 ( 1263)
  SS BOND              : bond        0.00239 (    4)
  SS BOND              : angle       0.36618 (    8)
  covalent geometry    : bond        0.00216 ( 9213)
  covalent geometry    : angle       0.49613 (12548)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  333 is missing expected H atoms. Skipping.
Evaluate side-chains
  188 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 173
  time to evaluate  : 1.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 SER cc_start: 0.8805 (t) cc_final: 0.8164 (p)
REVERT: B  188 MET cc_start: 0.8619 (mmm) cc_final: 0.8254 (mmm)
REVERT: B  219 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.8065 (mtt-85)
REVERT: E    3 GLN cc_start: 0.8041 (mp10) cc_final: 0.7776 (mp10)
REVERT: E  220 GLU cc_start: 0.7596 (mp0) cc_final: 0.6880 (mp0)
REVERT: G   18 GLN cc_start: 0.8495 (tp40) cc_final: 0.8100 (tp40)
REVERT: G   31 SER cc_start: 0.9467 (t) cc_final: 0.8997 (p)
REVERT: G   36 ASP cc_start: 0.8974 (m-30) cc_final: 0.8624 (m-30)
REVERT: R   80 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7542 (t70)
REVERT: R  139 VAL cc_start: 0.8820 (t) cc_final: 0.8608 (m)
REVERT: R  390 TYR cc_start: 0.8395 (m-10) cc_final: 0.8082 (m-10)
  outliers start: 15
  outliers final: 13
  residues processed: 183
  average time/residue: 0.4590
  time to fit residues: 117.1430
Evaluate side-chains
  178 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 164
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain R residue   80 ASP
Chi-restraints excluded: chain R residue  163 SER
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  203 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 31 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 107 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   chunk 109 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 102 optimal weight:    1.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** R 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.107800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.082055 restraints weight = 48429.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 2.91
r_work: 0.3014 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.5304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9217  Z= 0.176
  Angle     :  0.533   7.558  12556  Z= 0.284
  Chirality :  0.040   0.143   1443
  Planarity :  0.004   0.036   1549
  Dihedral  :  5.895  54.108   1831
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 13.33 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.96 (0.25), residues: 1107
  helix:  2.13 (0.26), residues: 388
  sheet: -0.35 (0.30), residues: 273
  loop :  0.08 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 211 
 HIS   0.005   0.001   HIS R 366 
 PHE   0.012   0.001   PHE R 201 
 TYR   0.019   0.001   TYR E 103 
 ARG   0.005   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03474 (  449)
  hydrogen bonds       : angle       4.40962 ( 1263)
  SS BOND              : bond        0.00227 (    4)
  SS BOND              : angle       0.58070 (    8)
  covalent geometry    : bond        0.00386 ( 9213)
  covalent geometry    : angle       0.53259 (12548)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  333 is missing expected H atoms. Skipping.
Evaluate side-chains
  182 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 164
  time to evaluate  : 1.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 SER cc_start: 0.8858 (t) cc_final: 0.8246 (p)
REVERT: B  118 ASP cc_start: 0.8039 (t0) cc_final: 0.7497 (p0)
REVERT: E    3 GLN cc_start: 0.8067 (mp10) cc_final: 0.7808 (mp10)
REVERT: E  220 GLU cc_start: 0.7552 (mp0) cc_final: 0.6822 (mp0)
REVERT: G   18 GLN cc_start: 0.8565 (tp40) cc_final: 0.8187 (tp40)
REVERT: G   31 SER cc_start: 0.9474 (t) cc_final: 0.9015 (p)
REVERT: G   36 ASP cc_start: 0.8973 (m-30) cc_final: 0.8627 (m-30)
REVERT: R   80 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7614 (t70)
REVERT: R  390 TYR cc_start: 0.8565 (m-10) cc_final: 0.8312 (m-10)
  outliers start: 18
  outliers final: 13
  residues processed: 174
  average time/residue: 0.4426
  time to fit residues: 107.1267
Evaluate side-chains
  180 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 166
  time to evaluate  : 1.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain R residue   80 ASP
Chi-restraints excluded: chain R residue  163 SER
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 74 optimal weight:    6.9990
   chunk 8 optimal weight:    0.7980
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
R 396 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.108979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.083274 restraints weight = 47933.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.92
r_work: 0.3037 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.5407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9217  Z= 0.126
  Angle     :  0.511   6.813  12556  Z= 0.272
  Chirality :  0.039   0.148   1443
  Planarity :  0.004   0.040   1549
  Dihedral  :  5.752  53.497   1831
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.54 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.97 (0.25), residues: 1107
  helix:  2.14 (0.26), residues: 388
  sheet: -0.38 (0.30), residues: 273
  loop :  0.11 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 211 
 HIS   0.007   0.001   HIS R 366 
 PHE   0.010   0.001   PHE R 201 
 TYR   0.016   0.001   TYR E 103 
 ARG   0.005   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03334 (  449)
  hydrogen bonds       : angle       4.34499 ( 1263)
  SS BOND              : bond        0.00226 (    4)
  SS BOND              : angle       0.47296 (    8)
  covalent geometry    : bond        0.00278 ( 9213)
  covalent geometry    : angle       0.51098 (12548)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  333 is missing expected H atoms. Skipping.
Evaluate side-chains
  190 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 174
  time to evaluate  : 1.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 SER cc_start: 0.8832 (t) cc_final: 0.8200 (p)
REVERT: B  118 ASP cc_start: 0.8095 (t0) cc_final: 0.7506 (p0)
REVERT: E    3 GLN cc_start: 0.8060 (mp10) cc_final: 0.7822 (mp10)
REVERT: E  220 GLU cc_start: 0.7544 (mp0) cc_final: 0.6810 (mp0)
REVERT: G   18 GLN cc_start: 0.8563 (tp40) cc_final: 0.8192 (tp40)
REVERT: G   31 SER cc_start: 0.9472 (t) cc_final: 0.9018 (p)
REVERT: G   36 ASP cc_start: 0.8955 (m-30) cc_final: 0.8608 (m-30)
REVERT: R   80 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7563 (t70)
REVERT: R  390 TYR cc_start: 0.8637 (m-10) cc_final: 0.8424 (m-10)
  outliers start: 16
  outliers final: 15
  residues processed: 184
  average time/residue: 0.4437
  time to fit residues: 113.8297
Evaluate side-chains
  184 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 168
  time to evaluate  : 1.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain R residue   80 ASP
Chi-restraints excluded: chain R residue  130 SER
Chi-restraints excluded: chain R residue  163 SER
Chi-restraints excluded: chain R residue  170 VAL
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0570
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 100 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.0702

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

Flipped N/Q/H residues before XYZ refinement:
R 396 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.109674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.083976 restraints weight = 47971.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 2.92
r_work: 0.3050 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.5506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9217  Z= 0.116
  Angle     :  0.502   6.137  12556  Z= 0.267
  Chirality :  0.039   0.146   1443
  Planarity :  0.004   0.040   1549
  Dihedral  :  5.592  52.527   1831
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 13.54 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.25), residues: 1107
  helix:  2.15 (0.27), residues: 389
  sheet: -0.27 (0.31), residues: 259
  loop :  0.09 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 366 
 PHE   0.009   0.001   PHE R 201 
 TYR   0.015   0.001   TYR E 103 
 ARG   0.005   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03262 (  449)
  hydrogen bonds       : angle       4.29343 ( 1263)
  SS BOND              : bond        0.00244 (    4)
  SS BOND              : angle       0.69436 (    8)
  covalent geometry    : bond        0.00256 ( 9213)
  covalent geometry    : angle       0.50169 (12548)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7662.38 seconds
wall clock time: 132 minutes 25.86 seconds (7945.86 seconds total)