Starting phenix.real_space_refine
on Thu Mar 13 23:29:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xbm_22120/03_2025/6xbm_22120.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xbm_22120/03_2025/6xbm_22120.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xbm_22120/03_2025/6xbm_22120.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xbm_22120/03_2025/6xbm_22120.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xbm_22120/03_2025/6xbm_22120.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xbm_22120/03_2025/6xbm_22120.cif"
  }
  resolution = 3.14
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     C    5880      2.51       5
     N    1543      2.21       5
     O    1724      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 63 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9211
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2618
          Classifications: {'peptide': 331}
          Link IDs: {'PTRANS': 10, 'TRANS': 320}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1736
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 212}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 407
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
    Chain: "S"
      Number of atoms: 1785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1785
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 58
          Unusual residues: {'CO1': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.90, per 1000 atoms: 0.64
  Number of scatterers: 9211
  At special positions: 0
  Unit cell: (105.664, 112.32, 126.464, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      64     16.00
     O    1724      8.00
     N    1543      7.00
     C    5880      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 193 " - pdb=" SG  CYS R 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 217 " - pdb=" SG  CYS R 295 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 314 " - pdb=" SG  CYS R 390 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.41
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2166

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 14 sheets defined
      36.2% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'R' and resid 223 through 254
    Processing helix  chain 'R' and resid 261 through 283
      removed outlier: 3.693A  pdb=" N   ILE R 266 " --> pdb=" O   TYR R 262 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   LEU R 267 " --> pdb=" O   PRO R 263 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   PHE R 268 " --> pdb=" O   ALA R 264 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 288 through 295
    Processing helix  chain 'R' and resid 312 through 345
      removed outlier: 3.557A  pdb=" N   ALA R 345 " --> pdb=" O   THR R 341 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 356 through 379
      Proline residue:  R 368  - end of helix
    Processing helix  chain 'R' and resid 396 through 433
      removed outlier: 3.959A  pdb=" N   ARG R 400 " --> pdb=" O   ASN R 396 " (cutoff:3.500A)
      Proline residue:  R 407  - end of helix
      removed outlier: 4.262A  pdb=" N   LYS R 430 " --> pdb=" O   LEU R 426 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   SER R 431 " --> pdb=" O   PHE R 427 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 438 through 496
      removed outlier: 4.483A  pdb=" N   ALA R 478 " --> pdb=" O   PHE R 474 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   GLU R 479 " --> pdb=" O   PHE R 475 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   ARG R 482 " --> pdb=" O   ALA R 478 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ARG R 485 " --> pdb=" O   GLU R 481 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLN R 491 " --> pdb=" O   TYR R 487 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ILE R 496 " --> pdb=" O   ALA R 492 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 514 through 534
      removed outlier: 4.434A  pdb=" N   GLU R 518 " --> pdb=" O   SER R 514 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 535 through 537
      No H-bonds generated for 'chain 'R' and resid 535 through 537'
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.720A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.640A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.535A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 242 through 255
      removed outlier: 3.504A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 4.139A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ILE A 278 " --> pdb=" O   PHE A 274 " (cutoff:3.500A)
      removed outlier: 4.833A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.716A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.786A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 351
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 10 through 24
      removed outlier: 3.877A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.770A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing sheet with id=AA1, first strand: chain 'R' and resid 381 through 383
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.755A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.983A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.892A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 5.983A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.645A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.270A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.728A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.593A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.766A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.703A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 278
      removed outlier: 6.519A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 315 through 317
      removed outlier: 6.612A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 4 through 7
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.557A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.725A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLY S 213 " --> pdb=" O   LEU S 233 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)

    446 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: 2.77

  Time building geometry restraints manager: 2.84 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1925
        1.33 -     1.45: 2224
        1.45 -     1.58: 5160
        1.58 -     1.70: 19
        1.70 -     1.82: 92
  Bond restraints: 9420
  Sorted by residual:
  bond pdb=" C14 CO1 R 702 "
       pdb=" C7  CO1 R 702 "
    ideal  model  delta    sigma   weight residual
    1.519  1.632 -0.113 2.00e-02 2.50e+03 3.18e+01
  bond pdb=" C14 CO1 R 701 "
       pdb=" C7  CO1 R 701 "
    ideal  model  delta    sigma   weight residual
    1.519  1.626 -0.107 2.00e-02 2.50e+03 2.87e+01
  bond pdb=" N   ILE B 270 "
       pdb=" CA  ILE B 270 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 9.30e-03 1.16e+04 1.77e+01
  bond pdb=" N   ILE B  93 "
       pdb=" CA  ILE B  93 "
    ideal  model  delta    sigma   weight residual
    1.460  1.492 -0.032 7.60e-03 1.73e+04 1.75e+01
  bond pdb=" C10 CO1 R 701 "
       pdb=" C17 CO1 R 701 "
    ideal  model  delta    sigma   weight residual
    1.535  1.619 -0.084 2.00e-02 2.50e+03 1.74e+01
  ... (remaining 9415 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 9011
        1.86 -     3.71: 3457
        3.71 -     5.57: 296
        5.57 -     7.42: 10
        7.42 -     9.28: 3
  Bond angle restraints: 12777
  Sorted by residual:
  angle pdb=" C   GLU R 194 "
        pdb=" N   VAL R 195 "
        pdb=" CA  VAL R 195 "
      ideal   model   delta    sigma   weight residual
     120.33  125.40   -5.07 8.00e-01 1.56e+00 4.02e+01
  angle pdb=" C   PHE R 526 "
        pdb=" N   GLY R 527 "
        pdb=" CA  GLY R 527 "
      ideal   model   delta    sigma   weight residual
     119.98  124.88   -4.90 1.11e+00 8.12e-01 1.95e+01
  angle pdb=" CA  ASP A 229 "
        pdb=" CB  ASP A 229 "
        pdb=" CG  ASP A 229 "
      ideal   model   delta    sigma   weight residual
     112.60  116.90   -4.30 1.00e+00 1.00e+00 1.85e+01
  angle pdb=" CA  THR R 466 "
        pdb=" CB  THR R 466 "
        pdb=" OG1 THR R 466 "
      ideal   model   delta    sigma   weight residual
     109.60  103.23    6.37 1.50e+00 4.44e-01 1.81e+01
  angle pdb=" C   THR A 295 "
        pdb=" N   TYR A 296 "
        pdb=" CA  TYR A 296 "
      ideal   model   delta    sigma   weight residual
     120.44  125.88   -5.44 1.30e+00 5.92e-01 1.75e+01
  ... (remaining 12772 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.81: 5059
       16.81 -    33.62: 457
       33.62 -    50.42: 91
       50.42 -    67.23: 21
       67.23 -    84.04: 9
  Dihedral angle restraints: 5637
    sinusoidal: 2266
      harmonic: 3371
  Sorted by residual:
  dihedral pdb=" CA  TYR S 223 "
           pdb=" C   TYR S 223 "
           pdb=" N   PRO S 224 "
           pdb=" CA  PRO S 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  122.21   57.79     0      5.00e+00 4.00e-02 1.34e+02
  dihedral pdb=" CB  CYS R 193 "
           pdb=" SG  CYS R 193 "
           pdb=" SG  CYS R 213 "
           pdb=" CB  CYS R 213 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  172.76  -79.76     1      1.00e+01 1.00e-02 7.89e+01
  dihedral pdb=" CA  GLU R 305 "
           pdb=" C   GLU R 305 "
           pdb=" N   PRO R 306 "
           pdb=" CA  PRO R 306 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.97   39.03     0      5.00e+00 4.00e-02 6.09e+01
  ... (remaining 5634 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 1037
       0.091 -    0.182: 377
       0.182 -    0.273: 12
       0.273 -    0.364: 1
       0.364 -    0.455: 6
  Chirality restraints: 1433
  Sorted by residual:
  chirality pdb=" C2  CO1 R 701 "
            pdb=" C1  CO1 R 701 "
            pdb=" C5  CO1 R 701 "
            pdb=" C6  CO1 R 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.78    0.45 2.00e-01 2.50e+01 5.17e+00
  chirality pdb=" C7  CO1 R 702 "
            pdb=" C14 CO1 R 702 "
            pdb=" C15 CO1 R 702 "
            pdb=" C3  CO1 R 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.86    3.31   -0.45 2.00e-01 2.50e+01 5.12e+00
  chirality pdb=" C2  CO1 R 702 "
            pdb=" C1  CO1 R 702 "
            pdb=" C5  CO1 R 702 "
            pdb=" C6  CO1 R 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.73    0.41 2.00e-01 2.50e+01 4.24e+00
  ... (remaining 1430 not shown)

  Planarity restraints: 1609
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA S 199 "    0.012 2.00e-02 2.50e+03   2.43e-02 5.91e+00
        pdb=" C   ALA S 199 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   ALA S 199 "    0.016 2.00e-02 2.50e+03
        pdb=" N   PHE S 200 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR R 262 "   -0.020 2.00e-02 2.50e+03   1.52e-02 4.61e+00
        pdb=" CG  TYR R 262 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TYR R 262 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR R 262 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR R 262 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR R 262 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR R 262 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR R 262 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  99 "    0.015 2.00e-02 2.50e+03   1.05e-02 2.75e+00
        pdb=" CG  TRP B  99 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  99 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  99 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  99 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  99 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  99 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  99 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  99 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  99 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1606 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 484
        2.75 -     3.29: 9199
        3.29 -     3.82: 14292
        3.82 -     4.36: 18891
        4.36 -     4.90: 31766
  Nonbonded interactions: 74632
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   SER S 196 "
            pdb=" O   ALA S 199 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OG1 THR R 349 "
            pdb=" O   ARG A  32 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" O   GLU R 292 "
            pdb=" NH2 ARG R 302 "
     model   vdw
     2.334 3.120
  ... (remaining 74627 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:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.060
  Set scattering table:                    0.110
  Process input model:                     24.580
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
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      :  0.014   0.113   9420  Z= 0.905
  Angle     :  1.682   9.278  12777  Z= 1.246
  Chirality :  0.083   0.455   1433
  Planarity :  0.004   0.038   1609
  Dihedral  : 13.683  84.039   3456
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.54 %
    Favored  : 95.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    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: -2.64 (0.22), residues: 1152
  helix: -0.79 (0.23), residues: 392
  sheet: -2.30 (0.30), residues: 243
  loop : -2.15 (0.25), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP B  99 
 HIS   0.008   0.001   HIS B  62 
 PHE   0.020   0.003   PHE R 285 
 TYR   0.037   0.003   TYR R 262 
 ARG   0.003   0.000   ARG S 179 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 192
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  228 GLN cc_start: 0.8679 (mt0) cc_final: 0.8309 (mp10)
REVERT: R  305 GLU cc_start: 0.6204 (tm-30) cc_final: 0.5867 (tm-30)
REVERT: R  344 LYS cc_start: 0.8350 (tttt) cc_final: 0.7831 (ttpp)
REVERT: R  519 LYS cc_start: 0.8079 (mttt) cc_final: 0.7877 (mtpp)
REVERT: A    9 ASP cc_start: 0.7813 (m-30) cc_final: 0.7256 (m-30)
REVERT: A  198 MET cc_start: 0.7863 (mtm) cc_final: 0.7524 (ttp)
REVERT: B    6 GLN cc_start: 0.7619 (pp30) cc_final: 0.7182 (pp30)
REVERT: B   29 THR cc_start: 0.8331 (m) cc_final: 0.7913 (p)
REVERT: B  197 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7814 (tpp80)
REVERT: G   18 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7838 (tp40)
REVERT: S   13 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8131 (tp40)
REVERT: S   19 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8298 (tttp)
REVERT: S   76 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8269 (mtmm)
REVERT: S   89 GLU cc_start: 0.7724 (mp0) cc_final: 0.7496 (mp0)
REVERT: S  174 GLN cc_start: 0.8494 (pt0) cc_final: 0.8144 (pt0)
REVERT: S  210 GLU cc_start: 0.7849 (mp0) cc_final: 0.7489 (mp0)
  outliers start: 1
  outliers final: 0
  residues processed: 193
  average time/residue: 0.2683
  time to fit residues: 67.2149
Evaluate side-chains
  144 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 29 optimal weight:    7.9990
   chunk 58 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
R 202 ASN
R 380 GLN
R 396 ASN
A  22 ASN
A 195 HIS
A 213 HIS
A 306 GLN
B  16 ASN
B 266 HIS
B 340 ASN
S 167 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.130179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.096667 restraints weight = 13183.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.19
r_work: 0.3024 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.1696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9420  Z= 0.202
  Angle     :  0.565   8.061  12777  Z= 0.290
  Chirality :  0.041   0.148   1433
  Planarity :  0.004   0.051   1609
  Dihedral  :  6.249  84.980   1399
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 10.90 %
    Favored  : 87.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    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: -1.07 (0.24), residues: 1152
  helix:  1.23 (0.26), residues: 403
  sheet: -1.90 (0.28), residues: 276
  loop : -1.61 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 206 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.015   0.001   PHE A 189 
 TYR   0.019   0.001   TYR S 178 
 ARG   0.004   0.000   ARG R 291 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 163
  time to evaluate  : 1.272 
Fit side-chains
   revert: symmetry clash
REVERT: R  228 GLN cc_start: 0.8720 (mt0) cc_final: 0.8384 (mp10)
REVERT: R  344 LYS cc_start: 0.8657 (tttt) cc_final: 0.8194 (ttpp)
REVERT: A   52 GLN cc_start: 0.7610 (mt0) cc_final: 0.7379 (mt0)
REVERT: B    8 ARG cc_start: 0.8240 (ttm170) cc_final: 0.7919 (mtp85)
REVERT: B  101 MET cc_start: 0.9296 (mtp) cc_final: 0.9085 (mtp)
REVERT: B  197 ARG cc_start: 0.8882 (mmm-85) cc_final: 0.8621 (tpp80)
REVERT: G   47 GLU cc_start: 0.8711 (mp0) cc_final: 0.8437 (mt-10)
REVERT: S   13 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8440 (tp40)
REVERT: S   76 LYS cc_start: 0.8987 (mmmm) cc_final: 0.8680 (mtmm)
REVERT: S  180 MET cc_start: 0.9013 (ptm) cc_final: 0.8639 (ptm)
REVERT: S  210 GLU cc_start: 0.8201 (mp0) cc_final: 0.7900 (mp0)
  outliers start: 17
  outliers final: 6
  residues processed: 170
  average time/residue: 0.2647
  time to fit residues: 59.9769
Evaluate side-chains
  153 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 147
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  237 PHE
Chi-restraints excluded: chain R residue  349 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  192 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0870
   chunk 43 optimal weight:    8.9990
   chunk 24 optimal weight:    7.9990
   chunk 112 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 6 optimal weight:    9.9990
   chunk 72 optimal weight:    0.3980
   overall best weight:    1.4762

-------------------------------------------------------------------------------
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**
A  22 ASN
A 306 GLN
B  91 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.127131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.094716 restraints weight = 13667.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 2.03
r_work: 0.2983 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9420  Z= 0.273
  Angle     :  0.578   9.006  12777  Z= 0.294
  Chirality :  0.042   0.147   1433
  Planarity :  0.004   0.052   1609
  Dihedral  :  6.289  89.404   1399
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 13.72 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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: -0.74 (0.25), residues: 1152
  helix:  1.58 (0.27), residues: 403
  sheet: -1.76 (0.28), residues: 291
  loop : -1.44 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  99 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.012   0.001   PHE B 235 
 TYR   0.016   0.002   TYR A 302 
 ARG   0.004   0.000   ARG B 150 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 153
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
REVERT: R  228 GLN cc_start: 0.8611 (mt0) cc_final: 0.8315 (mp10)
REVERT: R  230 MET cc_start: 0.8416 (tpp) cc_final: 0.7880 (tpp)
REVERT: R  344 LYS cc_start: 0.8757 (tttt) cc_final: 0.8381 (ttpp)
REVERT: A  242 ARG cc_start: 0.8917 (mtm-85) cc_final: 0.8716 (mtt90)
REVERT: A  302 TYR cc_start: 0.9260 (t80) cc_final: 0.8999 (t80)
REVERT: B    8 ARG cc_start: 0.8272 (ttm170) cc_final: 0.7957 (mtp85)
REVERT: G   22 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8379 (tt0)
REVERT: G   47 GLU cc_start: 0.8679 (mp0) cc_final: 0.8468 (mt-10)
REVERT: S   13 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8483 (tp40)
REVERT: S   73 ASP cc_start: 0.8440 (t70) cc_final: 0.8230 (t70)
REVERT: S  113 GLN cc_start: 0.8756 (tp40) cc_final: 0.8393 (mm-40)
REVERT: S  210 GLU cc_start: 0.8229 (mp0) cc_final: 0.7999 (mp0)
  outliers start: 23
  outliers final: 16
  residues processed: 165
  average time/residue: 0.2507
  time to fit residues: 55.5684
Evaluate side-chains
  161 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  237 PHE
Chi-restraints excluded: chain R residue  349 THR
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 85 optimal weight:    0.6980
   chunk 68 optimal weight:    0.0980
   chunk 56 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 78 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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**
A  22 ASN
** B 259 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 = 0.3657 r_free = 0.3657 target = 0.129155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.096753 restraints weight = 13446.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 1.99
r_work: 0.3023 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8714
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9420  Z= 0.197
  Angle     :  0.529   8.705  12777  Z= 0.270
  Chirality :  0.040   0.134   1433
  Planarity :  0.003   0.053   1609
  Dihedral  :  6.157  83.917   1399
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.53 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.25), residues: 1152
  helix:  1.75 (0.27), residues: 403
  sheet: -1.44 (0.29), residues: 260
  loop : -1.43 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 206 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.017   0.001   TYR A 296 
 ARG   0.002   0.000   ARG B 150 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 155
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
REVERT: R  228 GLN cc_start: 0.8588 (mt0) cc_final: 0.8323 (mp10)
REVERT: R  230 MET cc_start: 0.8389 (tpp) cc_final: 0.7904 (tpp)
REVERT: R  344 LYS cc_start: 0.8726 (tttt) cc_final: 0.8320 (ttpp)
REVERT: R  444 LYS cc_start: 0.8412 (tppt) cc_final: 0.8140 (tppt)
REVERT: A  187 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8752 (p)
REVERT: A  296 TYR cc_start: 0.8634 (t80) cc_final: 0.8375 (t80)
REVERT: B    8 ARG cc_start: 0.8270 (ttm170) cc_final: 0.7968 (mtt-85)
REVERT: G   47 GLU cc_start: 0.8697 (mp0) cc_final: 0.8489 (mt-10)
REVERT: S   13 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8506 (tp40)
REVERT: S  113 GLN cc_start: 0.8783 (tp40) cc_final: 0.8402 (mm-40)
REVERT: S  210 GLU cc_start: 0.8251 (mp0) cc_final: 0.7968 (mp0)
  outliers start: 24
  outliers final: 16
  residues processed: 169
  average time/residue: 0.2464
  time to fit residues: 56.3460
Evaluate side-chains
  160 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  237 PHE
Chi-restraints excluded: chain R residue  311 THR
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 82 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 52 optimal weight:    1.9990
   chunk 20 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    2.3388

-------------------------------------------------------------------------------
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**
A  22 ASN
** B 259 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 = 0.3621 r_free = 0.3621 target = 0.126694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.092628 restraints weight = 13529.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 2.07
r_work: 0.2935 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2795 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8806
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   9420  Z= 0.382
  Angle     :  0.596   9.194  12777  Z= 0.304
  Chirality :  0.043   0.164   1433
  Planarity :  0.004   0.058   1609
  Dihedral  :  6.346  83.977   1399
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 15.74 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    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: -0.55 (0.25), residues: 1152
  helix:  1.65 (0.27), residues: 403
  sheet: -1.56 (0.28), residues: 293
  loop : -1.31 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP S  47 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.014   0.001   PHE B 235 
 TYR   0.015   0.002   TYR A 296 
 ARG   0.004   0.000   ARG B 150 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 145
  time to evaluate  : 2.485 
Fit side-chains
   revert: symmetry clash
REVERT: R  228 GLN cc_start: 0.8596 (mt0) cc_final: 0.8284 (mp10)
REVERT: R  230 MET cc_start: 0.8365 (tpp) cc_final: 0.7938 (tpp)
REVERT: R  344 LYS cc_start: 0.8817 (tttt) cc_final: 0.8462 (ttpp)
REVERT: A  302 TYR cc_start: 0.9242 (t80) cc_final: 0.8845 (t80)
REVERT: B    8 ARG cc_start: 0.8362 (ttm170) cc_final: 0.7970 (mtp85)
REVERT: B   58 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.9063 (pt)
REVERT: B  312 ASP cc_start: 0.8218 (m-30) cc_final: 0.7957 (t0)
REVERT: G   47 GLU cc_start: 0.8706 (mp0) cc_final: 0.8473 (mt-10)
REVERT: G   48 ASP cc_start: 0.8671 (t0) cc_final: 0.8434 (t0)
REVERT: S  113 GLN cc_start: 0.8848 (tp40) cc_final: 0.8467 (mm-40)
REVERT: S  210 GLU cc_start: 0.8353 (mp0) cc_final: 0.8121 (mp0)
  outliers start: 31
  outliers final: 25
  residues processed: 161
  average time/residue: 0.2443
  time to fit residues: 53.8680
Evaluate side-chains
  165 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  237 PHE
Chi-restraints excluded: chain R residue  311 THR
Chi-restraints excluded: chain R residue  329 VAL
Chi-restraints excluded: chain R residue  349 THR
Chi-restraints excluded: chain R residue  392 VAL
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   chunk 83 optimal weight:    0.6980
   chunk 78 optimal weight:    0.5980
   chunk 106 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 93 optimal weight:    0.3980
   chunk 91 optimal weight:    0.4980
   chunk 13 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
R 396 ASN
A  22 ASN
A 306 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.128970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.096896 restraints weight = 13366.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 1.97
r_work: 0.3029 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9420  Z= 0.168
  Angle     :  0.527   9.214  12777  Z= 0.269
  Chirality :  0.040   0.133   1433
  Planarity :  0.003   0.053   1609
  Dihedral  :  6.139  82.466   1399
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.85 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    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: -0.27 (0.25), residues: 1152
  helix:  1.86 (0.27), residues: 403
  sheet: -1.34 (0.30), residues: 260
  loop : -1.24 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 206 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.009   0.001   PHE A 189 
 TYR   0.016   0.001   TYR A 296 
 ARG   0.002   0.000   ARG R 400 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
REVERT: R  228 GLN cc_start: 0.8583 (mt0) cc_final: 0.8313 (mp10)
REVERT: R  230 MET cc_start: 0.8325 (tpp) cc_final: 0.7960 (tpp)
REVERT: R  344 LYS cc_start: 0.8719 (tttt) cc_final: 0.8314 (ttpp)
REVERT: A  198 MET cc_start: 0.8607 (ttm) cc_final: 0.8383 (ttm)
REVERT: A  302 TYR cc_start: 0.9182 (t80) cc_final: 0.8755 (t80)
REVERT: B    8 ARG cc_start: 0.8319 (ttm170) cc_final: 0.8036 (mtt-85)
REVERT: G   22 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8268 (tt0)
REVERT: S  113 GLN cc_start: 0.8802 (tp40) cc_final: 0.8449 (mm-40)
REVERT: S  180 MET cc_start: 0.8924 (ptm) cc_final: 0.8637 (ptm)
REVERT: S  210 GLU cc_start: 0.8219 (mp0) cc_final: 0.7863 (mp0)
  outliers start: 24
  outliers final: 16
  residues processed: 157
  average time/residue: 0.3405
  time to fit residues: 73.1558
Evaluate side-chains
  153 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  237 PHE
Chi-restraints excluded: chain R residue  329 VAL
Chi-restraints excluded: chain R residue  349 THR
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 3 optimal weight:    9.9990
   chunk 39 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 103 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 306 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.128799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.096146 restraints weight = 13536.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 2.00
r_work: 0.3008 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2873 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9420  Z= 0.222
  Angle     :  0.533   9.452  12777  Z= 0.273
  Chirality :  0.040   0.139   1433
  Planarity :  0.004   0.058   1609
  Dihedral  :  6.156  81.920   1399
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 17.26 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    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: -0.24 (0.25), residues: 1152
  helix:  1.87 (0.27), residues: 403
  sheet: -1.31 (0.30), residues: 263
  loop : -1.20 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 206 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.009   0.001   PHE A 189 
 TYR   0.016   0.001   TYR A 296 
 ARG   0.010   0.000   ARG B 214 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  228 GLN cc_start: 0.8549 (mt0) cc_final: 0.8255 (mp10)
REVERT: R  230 MET cc_start: 0.8323 (tpp) cc_final: 0.7954 (tpp)
REVERT: R  344 LYS cc_start: 0.8753 (tttt) cc_final: 0.8355 (ttpp)
REVERT: A  198 MET cc_start: 0.8630 (ttm) cc_final: 0.8396 (ttm)
REVERT: B    8 ARG cc_start: 0.8345 (ttm170) cc_final: 0.8076 (mtt-85)
REVERT: B  312 ASP cc_start: 0.8129 (m-30) cc_final: 0.7919 (t0)
REVERT: G   22 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8268 (tt0)
REVERT: G   47 GLU cc_start: 0.8684 (mp0) cc_final: 0.8479 (mt-10)
REVERT: G   48 ASP cc_start: 0.8584 (t0) cc_final: 0.8372 (t0)
REVERT: S  113 GLN cc_start: 0.8823 (tp40) cc_final: 0.8466 (mm-40)
  outliers start: 26
  outliers final: 21
  residues processed: 164
  average time/residue: 0.2370
  time to fit residues: 52.8179
Evaluate side-chains
  162 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  237 PHE
Chi-restraints excluded: chain R residue  311 THR
Chi-restraints excluded: chain R residue  329 VAL
Chi-restraints excluded: chain R residue  349 THR
Chi-restraints excluded: chain R residue  392 VAL
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 94 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0870
   chunk 88 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 42 optimal weight:    0.4980
   chunk 73 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** B 259 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 = 0.3663 r_free = 0.3663 target = 0.129977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.098053 restraints weight = 13580.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 1.96
r_work: 0.3045 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8697
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9420  Z= 0.171
  Angle     :  0.526   9.976  12777  Z= 0.268
  Chirality :  0.040   0.133   1433
  Planarity :  0.003   0.053   1609
  Dihedral  :  6.088  81.649   1399
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.46 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    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: -0.10 (0.25), residues: 1152
  helix:  1.92 (0.27), residues: 404
  sheet: -1.16 (0.30), residues: 267
  loop : -1.11 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 206 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.008   0.001   PHE A 189 
 TYR   0.025   0.001   TYR A 302 
 ARG   0.009   0.000   ARG B 214 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  228 GLN cc_start: 0.8561 (mt0) cc_final: 0.8275 (mp10)
REVERT: R  230 MET cc_start: 0.8293 (tpp) cc_final: 0.7992 (tpp)
REVERT: R  344 LYS cc_start: 0.8683 (tttt) cc_final: 0.8289 (ttpp)
REVERT: R  457 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.6402 (t80)
REVERT: A  187 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8766 (p)
REVERT: B    8 ARG cc_start: 0.8328 (ttm170) cc_final: 0.8092 (mtt-85)
REVERT: G   22 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8259 (tt0)
REVERT: S  113 GLN cc_start: 0.8781 (tp40) cc_final: 0.8465 (mm-40)
REVERT: S  180 MET cc_start: 0.8892 (ptm) cc_final: 0.8590 (ptm)
REVERT: S  210 GLU cc_start: 0.8000 (mp0) cc_final: 0.7762 (mp0)
  outliers start: 24
  outliers final: 21
  residues processed: 165
  average time/residue: 0.2337
  time to fit residues: 52.5643
Evaluate side-chains
  164 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  237 PHE
Chi-restraints excluded: chain R residue  311 THR
Chi-restraints excluded: chain R residue  329 VAL
Chi-restraints excluded: chain R residue  349 THR
Chi-restraints excluded: chain R residue  392 VAL
Chi-restraints excluded: chain R residue  457 PHE
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 67 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 105 optimal weight:    8.9990
   chunk 51 optimal weight:    5.9990
   chunk 73 optimal weight:    0.8980
   chunk 104 optimal weight:    0.4980
   chunk 102 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 304 GLN
A 306 GLN
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.130439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.098282 restraints weight = 13377.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 1.96
r_work: 0.3046 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.2635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9420  Z= 0.184
  Angle     :  0.536  10.191  12777  Z= 0.276
  Chirality :  0.040   0.135   1433
  Planarity :  0.003   0.057   1609
  Dihedral  :  6.110  81.441   1399
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.36 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    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: -0.03 (0.25), residues: 1152
  helix:  1.97 (0.27), residues: 404
  sheet: -1.07 (0.30), residues: 267
  loop : -1.09 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 206 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.009   0.001   PHE B 234 
 TYR   0.021   0.001   TYR A 302 
 ARG   0.003   0.000   ARG B 314 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  228 GLN cc_start: 0.8578 (mt0) cc_final: 0.8292 (mp10)
REVERT: R  230 MET cc_start: 0.8274 (tpp) cc_final: 0.8006 (tpp)
REVERT: R  344 LYS cc_start: 0.8688 (tttt) cc_final: 0.8294 (ttpp)
REVERT: R  457 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.6383 (t80)
REVERT: A  187 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8753 (p)
REVERT: B    8 ARG cc_start: 0.8368 (ttm170) cc_final: 0.8041 (mtt-85)
REVERT: B  172 GLU cc_start: 0.7720 (pm20) cc_final: 0.7380 (pm20)
REVERT: G   22 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8337 (tt0)
REVERT: S  113 GLN cc_start: 0.8741 (tp40) cc_final: 0.8407 (mm-40)
REVERT: S  180 MET cc_start: 0.8918 (ptm) cc_final: 0.8613 (ptm)
  outliers start: 28
  outliers final: 23
  residues processed: 168
  average time/residue: 0.2249
  time to fit residues: 52.2845
Evaluate side-chains
  167 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 142
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  237 PHE
Chi-restraints excluded: chain R residue  265 VAL
Chi-restraints excluded: chain R residue  311 THR
Chi-restraints excluded: chain R residue  329 VAL
Chi-restraints excluded: chain R residue  349 THR
Chi-restraints excluded: chain R residue  392 VAL
Chi-restraints excluded: chain R residue  457 PHE
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 99 optimal weight:    0.5980
   chunk 29 optimal weight:    7.9990
   chunk 93 optimal weight:    2.9990
   chunk 111 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0060
   chunk 66 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 23 optimal weight:    0.2980
   chunk 59 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
R 433 HIS
A  22 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.130204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.098166 restraints weight = 13341.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 2.02
r_work: 0.3045 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9420  Z= 0.163
  Angle     :  0.547  10.490  12777  Z= 0.281
  Chirality :  0.040   0.162   1433
  Planarity :  0.003   0.054   1609
  Dihedral  :  6.112  81.509   1399
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.76 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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:  0.05 (0.25), residues: 1152
  helix:  1.95 (0.27), residues: 404
  sheet: -0.90 (0.30), residues: 265
  loop : -1.05 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 206 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.009   0.001   PHE B 151 
 TYR   0.022   0.001   TYR A 302 
 ARG   0.003   0.000   ARG B  19 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  228 GLN cc_start: 0.8593 (mt0) cc_final: 0.8325 (mp10)
REVERT: R  230 MET cc_start: 0.8265 (tpp) cc_final: 0.8012 (tpp)
REVERT: R  344 LYS cc_start: 0.8671 (tttt) cc_final: 0.8292 (ttpp)
REVERT: R  457 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.6421 (t80)
REVERT: B    8 ARG cc_start: 0.8353 (ttm170) cc_final: 0.8105 (mtt-85)
REVERT: B  260 GLU cc_start: 0.8469 (tt0) cc_final: 0.8089 (tt0)
REVERT: G   22 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8181 (tt0)
REVERT: S  113 GLN cc_start: 0.8728 (tp40) cc_final: 0.8402 (mm-40)
REVERT: S  180 MET cc_start: 0.8904 (ptm) cc_final: 0.8591 (ptm)
  outliers start: 24
  outliers final: 22
  residues processed: 166
  average time/residue: 0.2328
  time to fit residues: 52.8280
Evaluate side-chains
  165 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 142
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  237 PHE
Chi-restraints excluded: chain R residue  265 VAL
Chi-restraints excluded: chain R residue  311 THR
Chi-restraints excluded: chain R residue  312 LEU
Chi-restraints excluded: chain R residue  329 VAL
Chi-restraints excluded: chain R residue  349 THR
Chi-restraints excluded: chain R residue  392 VAL
Chi-restraints excluded: chain R residue  457 PHE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 72 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 105 optimal weight:    0.0000
   chunk 1 optimal weight:    0.0470
   chunk 93 optimal weight:    0.0970
   chunk 8 optimal weight:    4.9990
   chunk 96 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.3880

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 311 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.132894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.101750 restraints weight = 13544.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 1.97
r_work: 0.3096 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   9420  Z= 0.150
  Angle     :  0.534  10.710  12777  Z= 0.275
  Chirality :  0.040   0.151   1433
  Planarity :  0.003   0.057   1609
  Dihedral  :  6.092  82.004   1399
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.86 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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:  0.14 (0.25), residues: 1152
  helix:  2.02 (0.27), residues: 404
  sheet: -0.71 (0.31), residues: 263
  loop : -1.09 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 537 
 HIS   0.003   0.001   HIS B 311 
 PHE   0.009   0.001   PHE B 292 
 TYR   0.016   0.001   TYR A 302 
 ARG   0.008   0.000   ARG S 148 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5767.36 seconds
wall clock time: 101 minutes 49.84 seconds (6109.84 seconds total)