Starting phenix.real_space_refine
on Wed Feb  4 06:41:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vsa_65299/02_2026/9vsa_65299.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vsa_65299/02_2026/9vsa_65299.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vsa_65299/02_2026/9vsa_65299.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vsa_65299/02_2026/9vsa_65299.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vsa_65299/02_2026/9vsa_65299.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vsa_65299/02_2026/9vsa_65299.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.058
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      42      5.16       5
     C    5976      2.51       5
     N    1446      2.21       5
     O    1584      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9048
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 394, 3016
          Classifications: {'peptide': 394}
          Link IDs: {'PTRANS': 11, 'TRANS': 382}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.06, per 1000 atoms: 0.23
  Number of scatterers: 9048
  At special positions: 0
  Unit cell: (128.7, 132, 71.5, 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      42     16.00
     O    1584      8.00
     N    1446      7.00
     C    5976      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 358.8 milliseconds
  

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2184

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 0 sheets defined
      75.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 70
    Processing helix  chain 'A' and resid 80 through 88
      removed outlier: 3.505A  pdb=" N   ALA A  84 " --> pdb=" O   PRO A  80 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE A  86 " --> pdb=" O   ILE A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 105
      removed outlier: 3.714A  pdb=" N   ILE A  98 " --> pdb=" O   SER A  94 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY A 100 " --> pdb=" O   PRO A  96 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LEU A 103 " --> pdb=" O   PHE A  99 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU A 104 " --> pdb=" O   GLY A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 117
      removed outlier: 3.748A  pdb=" N   LEU A 109 " --> pdb=" O   GLY A 105 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   GLU A 111 " --> pdb=" O   THR A 107 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   THR A 117 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 136
      removed outlier: 3.511A  pdb=" N   THR A 135 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 148
      removed outlier: 3.524A  pdb=" N   ALA A 145 " --> pdb=" O   GLU A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 183
      removed outlier: 3.516A  pdb=" N   VAL A 157 " --> pdb=" O   LYS A 153 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ILE A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ASN A 168 " --> pdb=" O   SER A 164 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   VAL A 172 " --> pdb=" O   ASN A 168 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   LEU A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ALA A 183 " --> pdb=" O   CYS A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 217
      removed outlier: 4.102A  pdb=" N   ALA A 196 " --> pdb=" O   ASP A 192 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   VAL A 198 " --> pdb=" O   LYS A 194 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   ASN A 199 " --> pdb=" O   GLN A 195 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   PHE A 200 " --> pdb=" O   ALA A 196 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   CYS A 209 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
      Proline residue:  A 213  - end of helix
      removed outlier: 3.803A  pdb=" N   GLY A 217 " --> pdb=" O   PRO A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 223
      removed outlier: 5.139A  pdb=" N   ASN A 221 " --> pdb=" O   TYR A 218 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLU A 223 " --> pdb=" O   LYS A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 257
      removed outlier: 3.565A  pdb=" N   ASP A 231 " --> pdb=" O   ALA A 227 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLY A 239 " --> pdb=" O   SER A 235 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ILE A 242 " --> pdb=" O   ARG A 238 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   VAL A 243 " --> pdb=" O   GLY A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 263
      removed outlier: 3.811A  pdb=" N   LEU A 262 " --> pdb=" O   HIS A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 309
      removed outlier: 3.839A  pdb=" N   ALA A 290 " --> pdb=" O   TRP A 286 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL A 293 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL A 298 " --> pdb=" O   GLY A 294 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   GLU A 304 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   TYR A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 316
    Processing helix  chain 'A' and resid 320 through 327
    Processing helix  chain 'A' and resid 328 through 334
      removed outlier: 4.060A  pdb=" N   VAL A 332 " --> pdb=" O   LEU A 328 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   GLY A 333 " --> pdb=" O   LEU A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 3.795A  pdb=" N   VAL A 342 " --> pdb=" O   HIS A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 347
    Processing helix  chain 'A' and resid 349 through 367
      removed outlier: 3.687A  pdb=" N   SER A 353 " --> pdb=" O   LYS A 349 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLN A 363 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE A 364 " --> pdb=" O   SER A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 380
      removed outlier: 3.658A  pdb=" N   ILE A 373 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 406
      removed outlier: 3.649A  pdb=" N   CYS A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL A 397 " --> pdb=" O   GLY A 393 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   THR A 402 " --> pdb=" O   SER A 398 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU A 406 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 433
      removed outlier: 3.851A  pdb=" N   GLY A 416 " --> pdb=" O   HIS A 412 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A 418 " --> pdb=" O   MET A 414 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU A 419 " --> pdb=" O   LYS A 415 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU A 420 " --> pdb=" O   GLY A 416 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   TYR A 423 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE A 426 " --> pdb=" O   CYS A 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 70
    Processing helix  chain 'B' and resid 80 through 88
      removed outlier: 3.504A  pdb=" N   ALA B  84 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE B  86 " --> pdb=" O   ILE B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 105
      removed outlier: 3.714A  pdb=" N   ILE B  98 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY B 100 " --> pdb=" O   PRO B  96 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU B 103 " --> pdb=" O   PHE B  99 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU B 104 " --> pdb=" O   GLY B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 117
      removed outlier: 3.748A  pdb=" N   LEU B 109 " --> pdb=" O   GLY B 105 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   GLU B 111 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   THR B 117 " --> pdb=" O   VAL B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 136
      removed outlier: 3.511A  pdb=" N   THR B 135 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 148
      removed outlier: 3.524A  pdb=" N   ALA B 145 " --> pdb=" O   GLU B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 183
      removed outlier: 3.516A  pdb=" N   VAL B 157 " --> pdb=" O   LYS B 153 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ILE B 165 " --> pdb=" O   LEU B 161 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ASN B 168 " --> pdb=" O   SER B 164 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   VAL B 172 " --> pdb=" O   ASN B 168 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   LEU B 173 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ALA B 183 " --> pdb=" O   CYS B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 217
      removed outlier: 4.101A  pdb=" N   ALA B 196 " --> pdb=" O   ASP B 192 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   VAL B 198 " --> pdb=" O   LYS B 194 " (cutoff:3.500A)
      removed outlier: 4.955A  pdb=" N   ASN B 199 " --> pdb=" O   GLN B 195 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   PHE B 200 " --> pdb=" O   ALA B 196 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   CYS B 209 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      Proline residue:  B 213  - end of helix
      removed outlier: 3.803A  pdb=" N   GLY B 217 " --> pdb=" O   PRO B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 218 through 223
      removed outlier: 5.138A  pdb=" N   ASN B 221 " --> pdb=" O   TYR B 218 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLU B 223 " --> pdb=" O   LYS B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 257
      removed outlier: 3.565A  pdb=" N   ASP B 231 " --> pdb=" O   ALA B 227 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLY B 239 " --> pdb=" O   SER B 235 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ILE B 242 " --> pdb=" O   ARG B 238 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   VAL B 243 " --> pdb=" O   GLY B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 263
      removed outlier: 3.811A  pdb=" N   LEU B 262 " --> pdb=" O   HIS B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 309
      removed outlier: 3.839A  pdb=" N   ALA B 290 " --> pdb=" O   TRP B 286 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL B 293 " --> pdb=" O   PHE B 289 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL B 298 " --> pdb=" O   GLY B 294 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   GLU B 304 " --> pdb=" O   ALA B 300 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   TYR B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 316
    Processing helix  chain 'B' and resid 320 through 327
    Processing helix  chain 'B' and resid 328 through 334
      removed outlier: 4.060A  pdb=" N   VAL B 332 " --> pdb=" O   LEU B 328 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   GLY B 333 " --> pdb=" O   LEU B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 342
      removed outlier: 3.795A  pdb=" N   VAL B 342 " --> pdb=" O   HIS B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 347
    Processing helix  chain 'B' and resid 349 through 367
      removed outlier: 3.688A  pdb=" N   SER B 353 " --> pdb=" O   LYS B 349 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLN B 363 " --> pdb=" O   GLY B 359 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE B 364 " --> pdb=" O   SER B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 380
      removed outlier: 3.659A  pdb=" N   ILE B 373 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 406
      removed outlier: 3.648A  pdb=" N   CYS B 394 " --> pdb=" O   LEU B 390 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL B 397 " --> pdb=" O   GLY B 393 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   THR B 402 " --> pdb=" O   SER B 398 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU B 406 " --> pdb=" O   THR B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 433
      removed outlier: 3.852A  pdb=" N   GLY B 416 " --> pdb=" O   HIS B 412 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL B 418 " --> pdb=" O   MET B 414 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU B 419 " --> pdb=" O   LYS B 415 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU B 420 " --> pdb=" O   GLY B 416 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   TYR B 423 " --> pdb=" O   LEU B 419 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE B 426 " --> pdb=" O   CYS B 422 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 70
    Processing helix  chain 'C' and resid 80 through 88
      removed outlier: 3.505A  pdb=" N   ALA C  84 " --> pdb=" O   PRO C  80 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE C  86 " --> pdb=" O   ILE C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 94 through 105
      removed outlier: 3.714A  pdb=" N   ILE C  98 " --> pdb=" O   SER C  94 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY C 100 " --> pdb=" O   PRO C  96 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LEU C 103 " --> pdb=" O   PHE C  99 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU C 104 " --> pdb=" O   GLY C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 117
      removed outlier: 3.749A  pdb=" N   LEU C 109 " --> pdb=" O   GLY C 105 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   GLU C 111 " --> pdb=" O   THR C 107 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR C 117 " --> pdb=" O   VAL C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 127 through 136
      removed outlier: 3.511A  pdb=" N   THR C 135 " --> pdb=" O   LEU C 131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 148
      removed outlier: 3.525A  pdb=" N   ALA C 145 " --> pdb=" O   GLU C 141 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 183
      removed outlier: 3.517A  pdb=" N   VAL C 157 " --> pdb=" O   LYS C 153 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ILE C 165 " --> pdb=" O   LEU C 161 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ASN C 168 " --> pdb=" O   SER C 164 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   VAL C 172 " --> pdb=" O   ASN C 168 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   LEU C 173 " --> pdb=" O   LEU C 169 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ALA C 183 " --> pdb=" O   CYS C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 217
      removed outlier: 4.102A  pdb=" N   ALA C 196 " --> pdb=" O   ASP C 192 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   VAL C 198 " --> pdb=" O   LYS C 194 " (cutoff:3.500A)
      removed outlier: 4.955A  pdb=" N   ASN C 199 " --> pdb=" O   GLN C 195 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   PHE C 200 " --> pdb=" O   ALA C 196 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   CYS C 209 " --> pdb=" O   LEU C 205 " (cutoff:3.500A)
      Proline residue:  C 213  - end of helix
      removed outlier: 3.804A  pdb=" N   GLY C 217 " --> pdb=" O   PRO C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 218 through 223
      removed outlier: 5.138A  pdb=" N   ASN C 221 " --> pdb=" O   TYR C 218 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLU C 223 " --> pdb=" O   LYS C 220 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 225 through 257
      removed outlier: 3.565A  pdb=" N   ASP C 231 " --> pdb=" O   ALA C 227 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLY C 239 " --> pdb=" O   SER C 235 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ILE C 242 " --> pdb=" O   ARG C 238 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   VAL C 243 " --> pdb=" O   GLY C 239 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 263
      removed outlier: 3.811A  pdb=" N   LEU C 262 " --> pdb=" O   HIS C 259 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 284 through 309
      removed outlier: 3.839A  pdb=" N   ALA C 290 " --> pdb=" O   TRP C 286 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL C 293 " --> pdb=" O   PHE C 289 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL C 298 " --> pdb=" O   GLY C 294 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLU C 304 " --> pdb=" O   ALA C 300 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   TYR C 305 " --> pdb=" O   LEU C 301 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 310 through 316
    Processing helix  chain 'C' and resid 320 through 327
    Processing helix  chain 'C' and resid 328 through 334
      removed outlier: 4.061A  pdb=" N   VAL C 332 " --> pdb=" O   LEU C 328 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   GLY C 333 " --> pdb=" O   LEU C 329 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 342
      removed outlier: 3.795A  pdb=" N   VAL C 342 " --> pdb=" O   HIS C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 342 through 347
    Processing helix  chain 'C' and resid 349 through 367
      removed outlier: 3.687A  pdb=" N   SER C 353 " --> pdb=" O   LYS C 349 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLN C 363 " --> pdb=" O   GLY C 359 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ILE C 364 " --> pdb=" O   SER C 360 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 367 through 380
      removed outlier: 3.659A  pdb=" N   ILE C 373 " --> pdb=" O   VAL C 369 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 388 through 406
      removed outlier: 3.649A  pdb=" N   CYS C 394 " --> pdb=" O   LEU C 390 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL C 397 " --> pdb=" O   GLY C 393 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   THR C 402 " --> pdb=" O   SER C 398 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU C 406 " --> pdb=" O   THR C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 412 through 433
      removed outlier: 3.850A  pdb=" N   GLY C 416 " --> pdb=" O   HIS C 412 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   VAL C 418 " --> pdb=" O   MET C 414 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU C 419 " --> pdb=" O   LYS C 415 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU C 420 " --> pdb=" O   GLY C 416 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   TYR C 423 " --> pdb=" O   LEU C 419 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE C 426 " --> pdb=" O   CYS C 422 " (cutoff:3.500A)

    486 hydrogen bonds defined for protein.
    1440 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.41

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2745
        1.34 -     1.46: 1628
        1.46 -     1.57: 4795
        1.57 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 9228
  Sorted by residual:
  bond pdb=" C   PHE B  79 "
       pdb=" N   PRO B  80 "
    ideal  model  delta    sigma   weight residual
    1.337  1.365 -0.028 1.11e-02 8.12e+03 6.52e+00
  bond pdb=" C   PHE A  79 "
       pdb=" N   PRO A  80 "
    ideal  model  delta    sigma   weight residual
    1.337  1.364 -0.027 1.11e-02 8.12e+03 6.11e+00
  bond pdb=" C   PHE C  79 "
       pdb=" N   PRO C  80 "
    ideal  model  delta    sigma   weight residual
    1.337  1.363 -0.027 1.11e-02 8.12e+03 5.88e+00
  bond pdb=" CB  PRO B 370 "
       pdb=" CG  PRO B 370 "
    ideal  model  delta    sigma   weight residual
    1.492  1.411  0.081 5.00e-02 4.00e+02 2.62e+00
  bond pdb=" CB  PRO C 370 "
       pdb=" CG  PRO C 370 "
    ideal  model  delta    sigma   weight residual
    1.492  1.411  0.081 5.00e-02 4.00e+02 2.60e+00
  ... (remaining 9223 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 11866
        1.61 -     3.21: 566
        3.21 -     4.82: 75
        4.82 -     6.43: 30
        6.43 -     8.03: 12
  Bond angle restraints: 12549
  Sorted by residual:
  angle pdb=" C   SER A  94 "
        pdb=" N   GLN A  95 "
        pdb=" CA  GLN A  95 "
      ideal   model   delta    sigma   weight residual
     120.06  125.77   -5.71 1.19e+00 7.06e-01 2.30e+01
  angle pdb=" C   SER B  94 "
        pdb=" N   GLN B  95 "
        pdb=" CA  GLN B  95 "
      ideal   model   delta    sigma   weight residual
     120.06  125.76   -5.70 1.19e+00 7.06e-01 2.30e+01
  angle pdb=" C   SER C  94 "
        pdb=" N   GLN C  95 "
        pdb=" CA  GLN C  95 "
      ideal   model   delta    sigma   weight residual
     120.06  125.76   -5.70 1.19e+00 7.06e-01 2.29e+01
  angle pdb=" C   ARG C 260 "
        pdb=" N   GLN C 261 "
        pdb=" CA  GLN C 261 "
      ideal   model   delta    sigma   weight residual
     120.28  125.69   -5.41 1.44e+00 4.82e-01 1.41e+01
  angle pdb=" C   ARG B 260 "
        pdb=" N   GLN B 261 "
        pdb=" CA  GLN B 261 "
      ideal   model   delta    sigma   weight residual
     120.28  125.67   -5.39 1.44e+00 4.82e-01 1.40e+01
  ... (remaining 12544 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.25: 5069
       12.25 -    24.50: 283
       24.50 -    36.75: 39
       36.75 -    49.00: 9
       49.00 -    61.25: 3
  Dihedral angle restraints: 5403
    sinusoidal: 2013
      harmonic: 3390
  Sorted by residual:
  dihedral pdb=" CA  GLN A  52 "
           pdb=" C   GLN A  52 "
           pdb=" N   LYS A  53 "
           pdb=" CA  LYS A  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.47  -19.53     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  GLN B  52 "
           pdb=" C   GLN B  52 "
           pdb=" N   LYS B  53 "
           pdb=" CA  LYS B  53 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.48  -19.52     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  GLN C  52 "
           pdb=" C   GLN C  52 "
           pdb=" N   LYS C  53 "
           pdb=" CA  LYS C  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.48  -19.52     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 5400 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 790
       0.034 -    0.068: 594
       0.068 -    0.102: 100
       0.102 -    0.137: 52
       0.137 -    0.171: 15
  Chirality restraints: 1551
  Sorted by residual:
  chirality pdb=" CA  GLN A  95 "
            pdb=" N   GLN A  95 "
            pdb=" C   GLN A  95 "
            pdb=" CB  GLN A  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.28e-01
  chirality pdb=" CA  GLN C  95 "
            pdb=" N   GLN C  95 "
            pdb=" C   GLN C  95 "
            pdb=" CB  GLN C  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.24e-01
  chirality pdb=" CA  GLN B  95 "
            pdb=" N   GLN B  95 "
            pdb=" C   GLN B  95 "
            pdb=" CB  GLN B  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.23e-01
  ... (remaining 1548 not shown)

  Planarity restraints: 1524
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A  79 "    0.046 5.00e-02 4.00e+02   6.90e-02 7.61e+00
        pdb=" N   PRO A  80 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A  80 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A  80 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C  79 "   -0.046 5.00e-02 4.00e+02   6.90e-02 7.61e+00
        pdb=" N   PRO C  80 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B  79 "   -0.045 5.00e-02 4.00e+02   6.88e-02 7.58e+00
        pdb=" N   PRO B  80 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO B  80 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B  80 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1521 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 2884
        2.83 -     3.35: 7807
        3.35 -     3.87: 13500
        3.87 -     4.38: 16776
        4.38 -     4.90: 29184
  Nonbonded interactions: 70151
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 314 "
            pdb=" O   LEU C 319 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OG  SER A 314 "
            pdb=" O   LEU A 319 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OG  SER B 314 "
            pdb=" O   LEU B 319 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" O   TYR B 305 "
            pdb=" OG1 THR B 309 "
     model   vdw
     2.390 3.040
  nonbonded pdb=" O   TYR C 305 "
            pdb=" OG1 THR C 309 "
     model   vdw
     2.390 3.040
  ... (remaining 70146 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             1.250
  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:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.860
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.081   9228  Z= 0.248
  Angle     :  0.831   8.032  12549  Z= 0.460
  Chirality :  0.048   0.171   1551
  Planarity :  0.007   0.069   1524
  Dihedral  :  8.113  61.249   3219
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 0.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -6.78 (0.12), residues: 1170
  helix: -4.58 (0.06), residues: 879
  sheet:  None (None), residues: 0
  loop : -3.14 (0.28), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 238 
 TYR   0.032   0.002   TYR A 159 
 PHE   0.018   0.002   PHE A 263 
 TRP   0.020   0.003   TRP A 257 
 HIS   0.006   0.002   HIS B 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00614 ( 9228)
  covalent geometry    : angle       0.83116 (12549)
  hydrogen bonds       : bond        0.37234 (  486)
  hydrogen bonds       : angle      10.70996 ( 1440)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.7795 (mttt) cc_final: 0.6440 (tmtt)
REVERT: A  267 GLU cc_start: 0.7973 (tt0) cc_final: 0.7355 (mt-10)
REVERT: A  283 ILE cc_start: 0.8109 (mt) cc_final: 0.7718 (mm)
REVERT: A  434 LYS cc_start: 0.7885 (tttt) cc_final: 0.7446 (mttt)
REVERT: B   74 LYS cc_start: 0.7876 (mttt) cc_final: 0.6293 (tmtt)
REVERT: B  244 MET cc_start: 0.8855 (mtp) cc_final: 0.8460 (mtm)
REVERT: B  267 GLU cc_start: 0.7724 (tt0) cc_final: 0.7198 (mt-10)
REVERT: B  391 GLU cc_start: 0.8534 (mp0) cc_final: 0.7759 (mp0)
REVERT: B  414 MET cc_start: 0.9156 (tpt) cc_final: 0.8869 (mmm)
REVERT: C  111 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6717 (tp30)
REVERT: C  232 MET cc_start: 0.8360 (ttm) cc_final: 0.7848 (ttm)
REVERT: C  267 GLU cc_start: 0.7675 (tt0) cc_final: 0.7128 (mt-10)
REVERT: C  283 ILE cc_start: 0.8481 (mt) cc_final: 0.8269 (mp)
REVERT: C  334 ASN cc_start: 0.7698 (m-40) cc_final: 0.7448 (m-40)
REVERT: C  337 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7562 (mt-10)
REVERT: C  347 LYS cc_start: 0.8541 (mttt) cc_final: 0.8265 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.5805
  time to fit residues: 109.1602
Evaluate side-chains
  120 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    0.0170
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
** A  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 189 GLN
A 338 HIS
** B  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 189 GLN
** C  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 189 GLN
C 318 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.143610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.096633 restraints weight = 11025.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.2951 rms_B_bonded: 1.98
r_work: 0.2831 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9228  Z= 0.123
  Angle     :  0.519   5.034  12549  Z= 0.283
  Chirality :  0.038   0.113   1551
  Planarity :  0.005   0.046   1524
  Dihedral  :  4.357  17.295   1236
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  5.78 %
    Favored  : 92.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.81 (0.20), residues: 1170
  helix: -2.21 (0.14), residues: 885
  sheet:  None (None), residues: 0
  loop : -2.88 (0.29), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 190 
 TYR   0.025   0.001   TYR C 159 
 PHE   0.018   0.001   PHE B 178 
 TRP   0.011   0.001   TRP C 257 
 HIS   0.004   0.001   HIS C 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9228)
  covalent geometry    : angle       0.51892 (12549)
  hydrogen bonds       : bond        0.05542 (  486)
  hydrogen bonds       : angle       4.46000 ( 1440)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7667 (mmm)
REVERT: A   68 GLU cc_start: 0.8789 (tp30) cc_final: 0.8363 (tt0)
REVERT: A   74 LYS cc_start: 0.7405 (mttt) cc_final: 0.6090 (tmtt)
REVERT: A  255 GLN cc_start: 0.7310 (tt0) cc_final: 0.7055 (tp40)
REVERT: A  267 GLU cc_start: 0.7996 (tt0) cc_final: 0.7098 (mt-10)
REVERT: A  283 ILE cc_start: 0.7926 (mt) cc_final: 0.7526 (mt)
REVERT: A  316 LYS cc_start: 0.8466 (mptm) cc_final: 0.8130 (mmtm)
REVERT: A  434 LYS cc_start: 0.8043 (tttt) cc_final: 0.7227 (mttt)
REVERT: B   45 LYS cc_start: 0.7813 (tttp) cc_final: 0.7053 (mppt)
REVERT: B   74 LYS cc_start: 0.7368 (mttt) cc_final: 0.5899 (tmtt)
REVERT: B  114 SER cc_start: 0.7261 (m) cc_final: 0.6993 (p)
REVERT: B  147 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8026 (mp)
REVERT: B  195 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8102 (tp-100)
REVERT: B  267 GLU cc_start: 0.7642 (tt0) cc_final: 0.6804 (mt-10)
REVERT: B  334 ASN cc_start: 0.7340 (m-40) cc_final: 0.7104 (m110)
REVERT: B  414 MET cc_start: 0.9254 (tpt) cc_final: 0.8941 (mmm)
REVERT: C   45 LYS cc_start: 0.7718 (tptp) cc_final: 0.7185 (mppt)
REVERT: C   74 LYS cc_start: 0.7615 (mttt) cc_final: 0.6181 (tmtt)
REVERT: C  232 MET cc_start: 0.7879 (ttm) cc_final: 0.7487 (ttm)
  outliers start: 18
  outliers final: 1
  residues processed: 129
  average time/residue: 0.4985
  time to fit residues: 68.6507
Evaluate side-chains
  104 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain C residue  113 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 88 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 58 optimal weight:    8.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 168 ASN
A 334 ASN
** B  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 GLN
** C  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 255 GLN
C 334 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.138479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.091032 restraints weight = 10996.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 1.99
r_work: 0.2763 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2639 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9228  Z= 0.180
  Angle     :  0.553   5.316  12549  Z= 0.293
  Chirality :  0.041   0.124   1551
  Planarity :  0.005   0.043   1524
  Dihedral  :  4.216  17.437   1236
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  :  6.79 %
    Favored  : 91.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.22), residues: 1170
  helix: -0.89 (0.17), residues: 870
  sheet:  None (None), residues: 0
  loop : -2.90 (0.27), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 187 
 TYR   0.027   0.002   TYR C 159 
 PHE   0.014   0.002   PHE C 263 
 TRP   0.011   0.001   TRP B 286 
 HIS   0.005   0.002   HIS C 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 9228)
  covalent geometry    : angle       0.55271 (12549)
  hydrogen bonds       : bond        0.06353 (  486)
  hydrogen bonds       : angle       4.22167 ( 1440)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7745 (mmm)
REVERT: A   68 GLU cc_start: 0.8822 (tp30) cc_final: 0.8429 (tt0)
REVERT: A   74 LYS cc_start: 0.7617 (mttt) cc_final: 0.6200 (tmtt)
REVERT: A  255 GLN cc_start: 0.7441 (tt0) cc_final: 0.7152 (tp40)
REVERT: A  267 GLU cc_start: 0.7418 (tt0) cc_final: 0.6383 (mt-10)
REVERT: A  283 ILE cc_start: 0.8100 (mt) cc_final: 0.7775 (mt)
REVERT: A  311 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6815 (mp0)
REVERT: A  312 GLU cc_start: 0.8662 (tp30) cc_final: 0.8283 (mm-30)
REVERT: A  434 LYS cc_start: 0.7982 (tttt) cc_final: 0.7097 (mttt)
REVERT: A  435 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6304 (tp)
REVERT: B   45 LYS cc_start: 0.7791 (tttp) cc_final: 0.7010 (mppt)
REVERT: B   68 GLU cc_start: 0.8609 (tp30) cc_final: 0.8248 (tt0)
REVERT: B   74 LYS cc_start: 0.7740 (mttt) cc_final: 0.6115 (tmtt)
REVERT: B  267 GLU cc_start: 0.7619 (tt0) cc_final: 0.6792 (mt-10)
REVERT: B  334 ASN cc_start: 0.7603 (m-40) cc_final: 0.7228 (m110)
REVERT: B  414 MET cc_start: 0.9331 (tpt) cc_final: 0.9109 (mmm)
REVERT: B  435 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6878 (tp)
REVERT: C  232 MET cc_start: 0.8031 (ttm) cc_final: 0.7578 (ttm)
REVERT: C  435 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6182 (tp)
  outliers start: 21
  outliers final: 8
  residues processed: 125
  average time/residue: 0.4853
  time to fit residues: 64.7355
Evaluate side-chains
  111 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  435 LEU
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  176 SER
Chi-restraints excluded: chain C residue  435 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0870
   chunk 78 optimal weight:    8.9990
   chunk 71 optimal weight:    0.5980
   chunk 100 optimal weight:    0.4980
   chunk 19 optimal weight:    9.9990
   chunk 37 optimal weight:    0.6980
   chunk 79 optimal weight:    0.0970
   overall best weight:    0.3956

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

Flipped N/Q/H residues before XYZ refinement:
** A  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  67 GLN
B 255 GLN
C  67 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.142658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.095097 restraints weight = 11101.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 2.02
r_work: 0.2823 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2699 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9228  Z= 0.094
  Angle     :  0.444   4.922  12549  Z= 0.237
  Chirality :  0.036   0.130   1551
  Planarity :  0.004   0.038   1524
  Dihedral  :  3.785  15.234   1236
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  :  7.70 %
    Favored  : 90.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.24), residues: 1170
  helix:  0.03 (0.18), residues: 870
  sheet:  None (None), residues: 0
  loop : -2.82 (0.27), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 190 
 TYR   0.019   0.001   TYR C 159 
 PHE   0.014   0.001   PHE B 178 
 TRP   0.008   0.001   TRP C 286 
 HIS   0.002   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 ( 9228)
  covalent geometry    : angle       0.44438 (12549)
  hydrogen bonds       : bond        0.03733 (  486)
  hydrogen bonds       : angle       3.59138 ( 1440)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A   37 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7699 (mmm)
REVERT: A   45 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7707 (tppt)
REVERT: A   68 GLU cc_start: 0.8733 (tp30) cc_final: 0.8402 (tt0)
REVERT: A   74 LYS cc_start: 0.7565 (mttt) cc_final: 0.6139 (tmtt)
REVERT: A  194 LYS cc_start: 0.8391 (mmtt) cc_final: 0.8154 (mmtp)
REVERT: A  255 GLN cc_start: 0.7209 (tt0) cc_final: 0.6966 (tp40)
REVERT: A  267 GLU cc_start: 0.7664 (tt0) cc_final: 0.6677 (mt-10)
REVERT: A  283 ILE cc_start: 0.7978 (mt) cc_final: 0.7582 (mt)
REVERT: A  311 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6785 (mp0)
REVERT: A  434 LYS cc_start: 0.7953 (tttt) cc_final: 0.7024 (mttt)
REVERT: A  435 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6818 (tp)
REVERT: B   36 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7215 (m-40)
REVERT: B   45 LYS cc_start: 0.7782 (tttp) cc_final: 0.7027 (mppt)
REVERT: B   74 LYS cc_start: 0.7679 (mttt) cc_final: 0.6161 (tmtt)
REVERT: B  267 GLU cc_start: 0.7381 (tt0) cc_final: 0.6605 (mt-10)
REVERT: B  334 ASN cc_start: 0.7116 (m-40) cc_final: 0.6898 (m110)
REVERT: B  414 MET cc_start: 0.9280 (tpt) cc_final: 0.9036 (mmm)
REVERT: B  435 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6907 (tp)
REVERT: C   45 LYS cc_start: 0.7684 (mmmt) cc_final: 0.6830 (mppt)
REVERT: C  189 GLN cc_start: 0.8405 (mt0) cc_final: 0.8205 (mt0)
REVERT: C  232 MET cc_start: 0.7832 (ttm) cc_final: 0.7438 (ttm)
REVERT: C  267 GLU cc_start: 0.7491 (tt0) cc_final: 0.6737 (mt-10)
REVERT: C  435 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6049 (tp)
  outliers start: 22
  outliers final: 9
  residues processed: 127
  average time/residue: 0.5376
  time to fit residues: 73.0686
Evaluate side-chains
  117 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  435 LEU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  176 SER
Chi-restraints excluded: chain C residue  433 ASP
Chi-restraints excluded: chain C residue  435 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 79 optimal weight:    0.4980
   chunk 18 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 103 optimal weight:    0.7980
   chunk 29 optimal weight:    7.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 189 GLN
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 GLN
C 255 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.140414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.092809 restraints weight = 10989.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 2.02
r_work: 0.2773 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2648 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9228  Z= 0.151
  Angle     :  0.513   7.208  12549  Z= 0.271
  Chirality :  0.040   0.162   1551
  Planarity :  0.004   0.038   1524
  Dihedral  :  3.892  17.154   1236
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  :  8.81 %
    Favored  : 88.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.24), residues: 1170
  helix:  0.24 (0.18), residues: 870
  sheet:  None (None), residues: 0
  loop : -2.80 (0.27), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 187 
 TYR   0.026   0.001   TYR C 159 
 PHE   0.011   0.001   PHE B 254 
 TRP   0.009   0.001   TRP C 286 
 HIS   0.004   0.001   HIS C 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 9228)
  covalent geometry    : angle       0.51325 (12549)
  hydrogen bonds       : bond        0.05336 (  486)
  hydrogen bonds       : angle       3.90183 ( 1440)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A   37 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7910 (mmm)
REVERT: A   68 GLU cc_start: 0.8686 (tp30) cc_final: 0.8411 (tt0)
REVERT: A   74 LYS cc_start: 0.7687 (mttt) cc_final: 0.6174 (tmtt)
REVERT: A  255 GLN cc_start: 0.7503 (tt0) cc_final: 0.7195 (tp40)
REVERT: A  283 ILE cc_start: 0.8102 (mt) cc_final: 0.7805 (mt)
REVERT: A  312 GLU cc_start: 0.8719 (tp30) cc_final: 0.8430 (mm-30)
REVERT: A  434 LYS cc_start: 0.7944 (tttt) cc_final: 0.7104 (mttt)
REVERT: A  435 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6417 (tp)
REVERT: B   36 ASN cc_start: 0.7859 (OUTLIER) cc_final: 0.7369 (m-40)
REVERT: B   74 LYS cc_start: 0.7831 (mttt) cc_final: 0.6198 (tmtt)
REVERT: B  267 GLU cc_start: 0.7549 (tt0) cc_final: 0.6706 (mt-10)
REVERT: B  311 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7699 (mp0)
REVERT: B  334 ASN cc_start: 0.7486 (m-40) cc_final: 0.7250 (m110)
REVERT: B  414 MET cc_start: 0.9390 (tpt) cc_final: 0.9133 (mmm)
REVERT: B  435 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6921 (tp)
REVERT: C   45 LYS cc_start: 0.7718 (mmmt) cc_final: 0.6860 (mppt)
REVERT: C  267 GLU cc_start: 0.7583 (tt0) cc_final: 0.6814 (mt-10)
REVERT: C  312 GLU cc_start: 0.8667 (tp30) cc_final: 0.8317 (mm-30)
REVERT: C  433 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.6511 (m-30)
REVERT: C  435 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.6001 (tp)
  outliers start: 22
  outliers final: 9
  residues processed: 119
  average time/residue: 0.6418
  time to fit residues: 81.3139
Evaluate side-chains
  117 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  311 GLU
Chi-restraints excluded: chain B residue  435 LEU
Chi-restraints excluded: chain C residue   36 ASN
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  176 SER
Chi-restraints excluded: chain C residue  433 ASP
Chi-restraints excluded: chain C residue  435 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 83 optimal weight:    0.0770
   chunk 12 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.8340

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

Flipped N/Q/H residues before XYZ refinement:
B 255 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.142220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.094564 restraints weight = 10999.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.2878 rms_B_bonded: 2.04
r_work: 0.2754 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2630 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9228  Z= 0.116
  Angle     :  0.467   4.954  12549  Z= 0.247
  Chirality :  0.038   0.155   1551
  Planarity :  0.003   0.036   1524
  Dihedral  :  3.747  16.366   1236
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  9.02 %
    Favored  : 88.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.24), residues: 1170
  helix:  0.63 (0.18), residues: 870
  sheet:  None (None), residues: 0
  loop : -2.74 (0.27), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 187 
 TYR   0.024   0.001   TYR C 159 
 PHE   0.011   0.001   PHE B 178 
 TRP   0.008   0.001   TRP C 286 
 HIS   0.003   0.001   HIS B 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9228)
  covalent geometry    : angle       0.46651 (12549)
  hydrogen bonds       : bond        0.04460 (  486)
  hydrogen bonds       : angle       3.68766 ( 1440)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A   37 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7754 (mmm)
REVERT: A   68 GLU cc_start: 0.8676 (tp30) cc_final: 0.8386 (tt0)
REVERT: A   74 LYS cc_start: 0.7653 (mttt) cc_final: 0.6245 (tmtt)
REVERT: A  133 ASN cc_start: 0.7610 (t0) cc_final: 0.7304 (t0)
REVERT: A  255 GLN cc_start: 0.7284 (tt0) cc_final: 0.7001 (tp40)
REVERT: A  283 ILE cc_start: 0.8018 (mt) cc_final: 0.7691 (mt)
REVERT: A  312 GLU cc_start: 0.8640 (tp30) cc_final: 0.8344 (mm-30)
REVERT: A  329 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7777 (mp)
REVERT: A  434 LYS cc_start: 0.7885 (tttt) cc_final: 0.7044 (mtmt)
REVERT: A  435 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6408 (tp)
REVERT: B   36 ASN cc_start: 0.7567 (OUTLIER) cc_final: 0.6997 (m-40)
REVERT: B   68 GLU cc_start: 0.8533 (tp30) cc_final: 0.8290 (tt0)
REVERT: B   74 LYS cc_start: 0.7751 (mttt) cc_final: 0.6127 (tmtt)
REVERT: B  232 MET cc_start: 0.8146 (ttm) cc_final: 0.7945 (mtp)
REVERT: B  267 GLU cc_start: 0.7443 (tt0) cc_final: 0.6616 (mt-10)
REVERT: B  334 ASN cc_start: 0.7276 (m-40) cc_final: 0.7049 (m110)
REVERT: B  414 MET cc_start: 0.9331 (tpt) cc_final: 0.9078 (mmm)
REVERT: B  435 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6905 (tp)
REVERT: C   45 LYS cc_start: 0.7653 (mmmt) cc_final: 0.6936 (mppt)
REVERT: C  267 GLU cc_start: 0.7469 (tt0) cc_final: 0.6663 (mt-10)
REVERT: C  312 GLU cc_start: 0.8566 (tp30) cc_final: 0.8141 (mm-30)
REVERT: C  435 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5725 (tp)
  outliers start: 20
  outliers final: 9
  residues processed: 119
  average time/residue: 0.6162
  time to fit residues: 78.2010
Evaluate side-chains
  117 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  435 LEU
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  176 SER
Chi-restraints excluded: chain C residue  283 ILE
Chi-restraints excluded: chain C residue  435 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 112 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 2 optimal weight:    0.2980
   chunk 37 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0370
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.8460

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

Flipped N/Q/H residues before XYZ refinement:
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 GLN
C 195 GLN
C 255 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.142075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.094290 restraints weight = 10980.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 2.04
r_work: 0.2739 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2616 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9228  Z= 0.117
  Angle     :  0.464   4.977  12549  Z= 0.245
  Chirality :  0.038   0.125   1551
  Planarity :  0.003   0.036   1524
  Dihedral  :  3.699  16.535   1236
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  9.32 %
    Favored  : 88.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.25), residues: 1170
  helix:  0.86 (0.18), residues: 870
  sheet:  None (None), residues: 0
  loop : -2.69 (0.28), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 187 
 TYR   0.025   0.001   TYR C 159 
 PHE   0.011   0.001   PHE B 254 
 TRP   0.008   0.001   TRP C 286 
 HIS   0.003   0.001   HIS C 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9228)
  covalent geometry    : angle       0.46427 (12549)
  hydrogen bonds       : bond        0.04531 (  486)
  hydrogen bonds       : angle       3.67850 ( 1440)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A   37 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7705 (mmm)
REVERT: A   68 GLU cc_start: 0.8655 (tp30) cc_final: 0.8215 (tt0)
REVERT: A   74 LYS cc_start: 0.7580 (mttt) cc_final: 0.6136 (tmtt)
REVERT: A  133 ASN cc_start: 0.7605 (t0) cc_final: 0.7289 (t0)
REVERT: A  255 GLN cc_start: 0.7232 (tt0) cc_final: 0.6937 (tp40)
REVERT: A  283 ILE cc_start: 0.8027 (mt) cc_final: 0.7726 (mt)
REVERT: A  312 GLU cc_start: 0.8612 (tp30) cc_final: 0.8311 (mm-30)
REVERT: A  329 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7672 (mp)
REVERT: A  434 LYS cc_start: 0.7845 (tttt) cc_final: 0.7001 (mtmt)
REVERT: A  435 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6391 (tp)
REVERT: B   36 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.6878 (m-40)
REVERT: B   74 LYS cc_start: 0.7645 (mttt) cc_final: 0.6081 (tmtt)
REVERT: B  267 GLU cc_start: 0.7355 (tt0) cc_final: 0.6596 (mt-10)
REVERT: B  334 ASN cc_start: 0.7268 (m-40) cc_final: 0.7055 (m110)
REVERT: B  414 MET cc_start: 0.9307 (tpt) cc_final: 0.9052 (mmm)
REVERT: B  435 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6837 (tp)
REVERT: C  232 MET cc_start: 0.7984 (mtp) cc_final: 0.7435 (ttm)
REVERT: C  267 GLU cc_start: 0.7416 (tt0) cc_final: 0.6663 (mt-10)
REVERT: C  312 GLU cc_start: 0.8531 (tp30) cc_final: 0.8166 (mm-30)
REVERT: C  435 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.6267 (tp)
  outliers start: 20
  outliers final: 11
  residues processed: 116
  average time/residue: 0.5741
  time to fit residues: 70.7253
Evaluate side-chains
  116 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  435 LEU
Chi-restraints excluded: chain C residue   36 ASN
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  176 SER
Chi-restraints excluded: chain C residue  283 ILE
Chi-restraints excluded: chain C residue  435 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 101 optimal weight:    0.0970
   chunk 51 optimal weight:    0.2980
   chunk 4 optimal weight:    0.0970
   chunk 27 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 83 optimal weight:    0.8980
   chunk 73 optimal weight:    0.5980
   chunk 63 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.3576

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

Flipped N/Q/H residues before XYZ refinement:
B 255 GLN
C 195 GLN
C 255 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.146008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.098426 restraints weight = 10930.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 2.04
r_work: 0.2837 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2712 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.3634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9228  Z= 0.088
  Angle     :  0.427   4.993  12549  Z= 0.225
  Chirality :  0.036   0.110   1551
  Planarity :  0.003   0.035   1524
  Dihedral  :  3.514  14.653   1236
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  9.63 %
    Favored  : 88.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.25), residues: 1170
  helix:  1.21 (0.18), residues: 879
  sheet:  None (None), residues: 0
  loop : -2.64 (0.28), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 187 
 TYR   0.022   0.001   TYR C 159 
 PHE   0.011   0.001   PHE C 178 
 TRP   0.006   0.001   TRP C 286 
 HIS   0.002   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00185 ( 9228)
  covalent geometry    : angle       0.42656 (12549)
  hydrogen bonds       : bond        0.03413 (  486)
  hydrogen bonds       : angle       3.37127 ( 1440)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A   37 MET cc_start: 0.8058 (mmm) cc_final: 0.7742 (mmm)
REVERT: A   74 LYS cc_start: 0.7612 (mttt) cc_final: 0.6163 (tmtt)
REVERT: A  133 ASN cc_start: 0.7515 (t0) cc_final: 0.7209 (t0)
REVERT: A  255 GLN cc_start: 0.7354 (tt0) cc_final: 0.7068 (tp40)
REVERT: A  283 ILE cc_start: 0.7968 (mt) cc_final: 0.7690 (tp)
REVERT: A  312 GLU cc_start: 0.8659 (tp30) cc_final: 0.8441 (mm-30)
REVERT: A  329 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7770 (mp)
REVERT: A  434 LYS cc_start: 0.7881 (tttt) cc_final: 0.7033 (mtmt)
REVERT: A  435 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6419 (tp)
REVERT: B   36 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.6985 (m-40)
REVERT: B   68 GLU cc_start: 0.8505 (tp30) cc_final: 0.8255 (tt0)
REVERT: B   74 LYS cc_start: 0.7775 (mttt) cc_final: 0.6227 (tmtt)
REVERT: B  267 GLU cc_start: 0.7489 (tt0) cc_final: 0.6644 (mt-10)
REVERT: B  414 MET cc_start: 0.9292 (tpt) cc_final: 0.9011 (mmm)
REVERT: B  435 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6847 (tp)
REVERT: C   45 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7070 (mppt)
REVERT: C  232 MET cc_start: 0.8032 (mtp) cc_final: 0.7494 (ttm)
REVERT: C  267 GLU cc_start: 0.7474 (tt0) cc_final: 0.6741 (mt-10)
REVERT: C  312 GLU cc_start: 0.8495 (tp30) cc_final: 0.8207 (mm-30)
REVERT: C  435 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6231 (tp)
  outliers start: 20
  outliers final: 5
  residues processed: 125
  average time/residue: 0.5655
  time to fit residues: 75.4848
Evaluate side-chains
  115 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  435 LEU
Chi-restraints excluded: chain C residue   45 LYS
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue  176 SER
Chi-restraints excluded: chain C residue  435 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 2 optimal weight:   20.0000
   chunk 81 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0060
   chunk 91 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    1.6002

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
B 334 ASN
C 189 GLN
C 255 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.138336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.090605 restraints weight = 10969.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.2811 rms_B_bonded: 2.02
r_work: 0.2684 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2562 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.3365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9228  Z= 0.179
  Angle     :  0.523   5.007  12549  Z= 0.274
  Chirality :  0.041   0.117   1551
  Planarity :  0.004   0.046   1524
  Dihedral  :  3.804  17.376   1236
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 2.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 10.94 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.25), residues: 1170
  helix:  0.96 (0.18), residues: 870
  sheet:  None (None), residues: 0
  loop : -2.57 (0.28), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 187 
 TYR   0.034   0.001   TYR C 159 
 PHE   0.014   0.002   PHE A 344 
 TRP   0.011   0.001   TRP A 286 
 HIS   0.004   0.002   HIS A 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 9228)
  covalent geometry    : angle       0.52289 (12549)
  hydrogen bonds       : bond        0.05545 (  486)
  hydrogen bonds       : angle       3.89475 ( 1440)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A   37 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7903 (mmm)
REVERT: A   74 LYS cc_start: 0.7746 (mttt) cc_final: 0.6106 (tmtt)
REVERT: A  133 ASN cc_start: 0.7764 (t0) cc_final: 0.7504 (t0)
REVERT: A  255 GLN cc_start: 0.7526 (tt0) cc_final: 0.7182 (tp40)
REVERT: A  312 GLU cc_start: 0.8651 (tp30) cc_final: 0.8367 (mm-30)
REVERT: A  329 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7837 (mp)
REVERT: A  434 LYS cc_start: 0.7918 (tttt) cc_final: 0.7120 (mtmm)
REVERT: A  435 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6357 (tp)
REVERT: B   36 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7176 (m-40)
REVERT: B  267 GLU cc_start: 0.7423 (tt0) cc_final: 0.6678 (mt-10)
REVERT: B  414 MET cc_start: 0.9368 (tpt) cc_final: 0.9128 (mmm)
REVERT: B  435 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6832 (tp)
REVERT: C  232 MET cc_start: 0.8199 (mtp) cc_final: 0.7648 (ttm)
REVERT: C  267 GLU cc_start: 0.7557 (tt0) cc_final: 0.6766 (mt-10)
REVERT: C  312 GLU cc_start: 0.8498 (tp30) cc_final: 0.8122 (mm-30)
REVERT: C  435 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6240 (tp)
  outliers start: 18
  outliers final: 7
  residues processed: 118
  average time/residue: 0.5818
  time to fit residues: 73.3719
Evaluate side-chains
  115 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  435 LEU
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue  176 SER
Chi-restraints excluded: chain C residue  435 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 85 optimal weight:    0.0980
   chunk 67 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 64 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 114 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 255 GLN
B 334 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.141653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.094025 restraints weight = 10878.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.2879 rms_B_bonded: 1.99
r_work: 0.2755 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2632 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.3593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9228  Z= 0.105
  Angle     :  0.450   5.018  12549  Z= 0.238
  Chirality :  0.038   0.112   1551
  Planarity :  0.004   0.049   1524
  Dihedral  :  3.626  15.667   1236
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 11.35 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.25), residues: 1170
  helix:  1.26 (0.18), residues: 870
  sheet:  None (None), residues: 0
  loop : -2.53 (0.28), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 190 
 TYR   0.030   0.001   TYR C 159 
 PHE   0.013   0.001   PHE B 115 
 TRP   0.008   0.001   TRP A 286 
 HIS   0.002   0.001   HIS C 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 9228)
  covalent geometry    : angle       0.44996 (12549)
  hydrogen bonds       : bond        0.04131 (  486)
  hydrogen bonds       : angle       3.56966 ( 1440)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A   37 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7591 (mmm)
REVERT: A   74 LYS cc_start: 0.7624 (mttt) cc_final: 0.6028 (tmtt)
REVERT: A  255 GLN cc_start: 0.7156 (tt0) cc_final: 0.6879 (tp40)
REVERT: A  312 GLU cc_start: 0.8574 (tp30) cc_final: 0.8264 (mm-30)
REVERT: A  329 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7679 (mp)
REVERT: A  434 LYS cc_start: 0.7862 (tttt) cc_final: 0.7011 (mtmt)
REVERT: A  435 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6312 (tp)
REVERT: B   36 ASN cc_start: 0.7355 (OUTLIER) cc_final: 0.6821 (m-40)
REVERT: B  267 GLU cc_start: 0.7389 (tt0) cc_final: 0.6557 (mt-10)
REVERT: B  435 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6908 (tp)
REVERT: C  232 MET cc_start: 0.7953 (mtp) cc_final: 0.7400 (ttm)
REVERT: C  267 GLU cc_start: 0.7408 (tt0) cc_final: 0.6665 (mt-10)
REVERT: C  312 GLU cc_start: 0.8494 (tp30) cc_final: 0.8094 (mm-30)
REVERT: C  435 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6312 (tp)
  outliers start: 14
  outliers final: 7
  residues processed: 116
  average time/residue: 0.5936
  time to fit residues: 73.3229
Evaluate side-chains
  114 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  435 LEU
Chi-restraints excluded: chain C residue   36 ASN
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue  176 SER
Chi-restraints excluded: chain C residue  435 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 23 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    1.1188

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
B 168 ASN
B 255 GLN
B 334 ASN
C 255 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.139667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.091986 restraints weight = 10810.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.2832 rms_B_bonded: 2.01
r_work: 0.2705 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2583 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.3517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9228  Z= 0.137
  Angle     :  0.486   4.999  12549  Z= 0.256
  Chirality :  0.040   0.113   1551
  Planarity :  0.004   0.040   1524
  Dihedral  :  3.714  16.898   1236
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.25 %
    Favored  : 87.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.25), residues: 1170
  helix:  1.17 (0.18), residues: 870
  sheet:  None (None), residues: 0
  loop : -2.50 (0.28), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 190 
 TYR   0.036   0.001   TYR C 159 
 PHE   0.013   0.001   PHE B 115 
 TRP   0.010   0.001   TRP A 286 
 HIS   0.004   0.001   HIS B 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 9228)
  covalent geometry    : angle       0.48597 (12549)
  hydrogen bonds       : bond        0.04928 (  486)
  hydrogen bonds       : angle       3.75684 ( 1440)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2958.15 seconds
wall clock time: 51 minutes 8.54 seconds (3068.54 seconds total)