Starting phenix.real_space_refine
on Wed Sep 17 14:29:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fl7_50532/09_2025/9fl7_50532.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fl7_50532/09_2025/9fl7_50532.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fl7_50532/09_2025/9fl7_50532.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fl7_50532/09_2025/9fl7_50532.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fl7_50532/09_2025/9fl7_50532.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fl7_50532/09_2025/9fl7_50532.cif"
  }
  resolution = 4.3
  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=  -0.001 sd=   0.153
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      34      5.16       5
     C    5666      2.51       5
     N    1584      2.21       5
     O    1677      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8969
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3499
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 453, 3499
          Classifications: {'peptide': 453}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 429}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 445, 3442
          Classifications: {'peptide': 445}
          Link IDs: {'PTRANS': 21, 'TRANS': 423}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1834
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 219}
    Chain: "A"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 97
          Unusual residues: {'FAD': 1, 'NAD': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 97
          Unusual residues: {'FAD': 1, 'NAD': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.56, per 1000 atoms: 0.29
  Number of scatterers: 8969
  At special positions: 0
  Unit cell: (86.7, 122.4, 119, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      34     16.00
     P       8     15.00
     O    1677      8.00
     N    1584      7.00
     C    5666      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  42 " - pdb=" SG  CYS D  92 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.10
  Conformation dependent library (CDL) restraints added in 339.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2062

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 17 sheets defined
      34.7% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 140 through 154
    Processing helix  chain 'A' and resid 172 through 176
    Processing helix  chain 'A' and resid 186 through 191
    Processing helix  chain 'A' and resid 216 through 220
      removed outlier: 3.545A  pdb=" N   ILE A 220 " --> pdb=" O   LEU A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 273
      removed outlier: 3.626A  pdb=" N   ASP A 271 " --> pdb=" O   LEU A 267 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA A 273 " --> pdb=" O   ALA A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 279
      removed outlier: 3.709A  pdb=" N   LYS A 278 " --> pdb=" O   GLY A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 300
    Processing helix  chain 'A' and resid 309 through 327
      removed outlier: 3.511A  pdb=" N   SER A 313 " --> pdb=" O   GLY A 309 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LYS A 322 " --> pdb=" O   ALA A 318 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   ALA A 325 " --> pdb=" O   ARG A 321 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   LEU A 326 " --> pdb=" O   LYS A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 358
      removed outlier: 4.256A  pdb=" N   GLU A 354 " --> pdb=" O   ASN A 350 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LYS A 355 " --> pdb=" O   TRP A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 411
      removed outlier: 4.136A  pdb=" N   LYS A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   THR A 409 " --> pdb=" O   GLU A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 470
      removed outlier: 3.779A  pdb=" N   THR A 470 " --> pdb=" O   GLY A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 595
      removed outlier: 3.754A  pdb=" N   ALA A 588 " --> pdb=" O   ARG A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 609
      removed outlier: 3.762A  pdb=" N   VAL A 604 " --> pdb=" O   ASP A 600 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   PHE A 608 " --> pdb=" O   VAL A 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 154
      removed outlier: 3.525A  pdb=" N   PHE B 144 " --> pdb=" O   GLY B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 178
      removed outlier: 4.322A  pdb=" N   SER B 176 " --> pdb=" O   ARG B 172 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LYS B 177 " --> pdb=" O   PRO B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 182
    Processing helix  chain 'B' and resid 186 through 191
    Processing helix  chain 'B' and resid 267 through 272
      removed outlier: 3.527A  pdb=" N   ARG B 272 " --> pdb=" O   SER B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 280
    Processing helix  chain 'B' and resid 286 through 300
      removed outlier: 4.336A  pdb=" N   ARG B 298 " --> pdb=" O   GLU B 294 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   GLU B 299 " --> pdb=" O   LYS B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 327
      removed outlier: 3.584A  pdb=" N   SER B 313 " --> pdb=" O   GLY B 309 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ALA B 318 " --> pdb=" O   GLU B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 359
      removed outlier: 4.319A  pdb=" N   GLU B 354 " --> pdb=" O   ASN B 350 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   LYS B 355 " --> pdb=" O   TRP B 351 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ARG B 357 " --> pdb=" O   MET B 353 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLU B 359 " --> pdb=" O   LYS B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 471
      removed outlier: 3.774A  pdb=" N   THR B 470 " --> pdb=" O   GLY B 466 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   GLY B 471 " --> pdb=" O   GLU B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 584 through 595
      removed outlier: 3.669A  pdb=" N   ALA B 588 " --> pdb=" O   ARG B 584 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LYS B 590 " --> pdb=" O   PRO B 586 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY B 595 " --> pdb=" O   ILE B 591 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 601 through 606
    Processing helix  chain 'B' and resid 607 through 609
      No H-bonds generated for 'chain 'B' and resid 607 through 609'
    Processing helix  chain 'D' and resid 27 through 40
      Proline residue:  D  33  - end of helix
    Processing helix  chain 'D' and resid 47 through 57
      removed outlier: 3.680A  pdb=" N   GLY D  57 " --> pdb=" O   MET D  53 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 70
    Processing helix  chain 'D' and resid 77 through 89
      removed outlier: 3.554A  pdb=" N   THR D  89 " --> pdb=" O   LYS D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 93
    Processing helix  chain 'D' and resid 104 through 118
      removed outlier: 3.705A  pdb=" N   GLU D 109 " --> pdb=" O   VAL D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 131 through 141
    Processing helix  chain 'D' and resid 179 through 194
    Processing helix  chain 'D' and resid 196 through 203
      removed outlier: 3.644A  pdb=" N   TYR D 200 " --> pdb=" O   PRO D 196 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS D 203 " --> pdb=" O   GLU D 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 215 through 230
      removed outlier: 3.728A  pdb=" N   LYS D 229 " --> pdb=" O   ALA D 225 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ALA D 230 " --> pdb=" O   ALA D 226 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132
    Processing sheet with id=AA2, first strand: chain 'A' and resid 224 through 229
      removed outlier: 3.761A  pdb=" N   ALA A 226 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   SER A 163 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ARG A 430 " --> pdb=" O   ILE A 433 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   VAL A 435 " --> pdb=" O   GLN A 428 " (cutoff:3.500A)
      removed outlier: 4.944A  pdb=" N   GLN A 428 " --> pdb=" O   VAL A 435 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 264
      removed outlier: 3.737A  pdb=" N   GLU A 401 " --> pdb=" O   THR A 263 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 281 through 282
      removed outlier: 3.522A  pdb=" N   THR A 282 " --> pdb=" O   ILE A 394 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ALA A 396 " --> pdb=" O   THR A 282 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   SER A 302 " --> pdb=" O   HIS A 393 " (cutoff:3.500A)
      removed outlier: 8.363A  pdb=" N   VAL A 395 " --> pdb=" O   SER A 302 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   THR A 304 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ILE A 303 " --> pdb=" O   GLU A 329 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU A 333 " --> pdb=" O   ILE A 305 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 369 through 375
      removed outlier: 3.552A  pdb=" N   ILE A 381 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   VAL A 389 " --> pdb=" O   ILE A 381 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 442 through 443
    Processing sheet with id=AA7, first strand: chain 'A' and resid 481 through 486
      removed outlier: 3.884A  pdb=" N   VAL A 490 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   TYR A 567 " --> pdb=" O   VAL A 574 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   ILE A 576 " --> pdb=" O   ILE A 565 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   ILE A 565 " --> pdb=" O   ILE A 576 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   LEU A 578 " --> pdb=" O   GLY A 563 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   GLY A 563 " --> pdb=" O   LEU A 578 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   LYS A 562 " --> pdb=" O   ALA A 509 " (cutoff:3.500A)
      removed outlier: 7.592A  pdb=" N   MET D 237 " --> pdb=" O   THR A 504 " (cutoff:3.500A)
      removed outlier: 5.887A  pdb=" N   GLY A 506 " --> pdb=" O   MET D 237 " (cutoff:3.500A)
      removed outlier: 7.387A  pdb=" N   ILE D 239 " --> pdb=" O   GLY A 506 " (cutoff:3.500A)
      removed outlier: 5.717A  pdb=" N   PHE A 508 " --> pdb=" O   ILE D 239 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 224 through 228
      removed outlier: 3.740A  pdb=" N   VAL B 159 " --> pdb=" O   GLY B 224 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   VAL B 132 " --> pdb=" O   ARG B 158 " (cutoff:3.500A)
      removed outlier: 7.958A  pdb=" N   LEU B 160 " --> pdb=" O   VAL B 132 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   PHE B 134 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
      removed outlier: 8.164A  pdb=" N   VAL B 162 " --> pdb=" O   PHE B 134 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   LEU B 136 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
      removed outlier: 8.550A  pdb=" N   HIS B 131 " --> pdb=" O   TYR B 253 " (cutoff:3.500A)
      removed outlier: 9.901A  pdb=" N   LYS B 255 " --> pdb=" O   HIS B 131 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   LEU B 257 " --> pdb=" O   PRO B 133 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   LEU B 135 " --> pdb=" O   LEU B 257 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LYS B 244 " --> pdb=" O   GLN B 235 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   GLN B 235 " --> pdb=" O   LYS B 244 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 224 through 228
      removed outlier: 3.740A  pdb=" N   VAL B 159 " --> pdb=" O   GLY B 224 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   VAL B 132 " --> pdb=" O   ARG B 158 " (cutoff:3.500A)
      removed outlier: 7.958A  pdb=" N   LEU B 160 " --> pdb=" O   VAL B 132 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   PHE B 134 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
      removed outlier: 8.164A  pdb=" N   VAL B 162 " --> pdb=" O   PHE B 134 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   LEU B 136 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
      removed outlier: 8.550A  pdb=" N   HIS B 131 " --> pdb=" O   TYR B 253 " (cutoff:3.500A)
      removed outlier: 9.901A  pdb=" N   LYS B 255 " --> pdb=" O   HIS B 131 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   LEU B 257 " --> pdb=" O   PRO B 133 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   LEU B 135 " --> pdb=" O   LEU B 257 " (cutoff:3.500A)
      removed outlier: 8.815A  pdb=" N   TRP B 434 " --> pdb=" O   GLU B 254 " (cutoff:3.500A)
      removed outlier: 7.405A  pdb=" N   CYS B 256 " --> pdb=" O   TRP B 434 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 192 through 194
    Processing sheet with id=AB2, first strand: chain 'B' and resid 262 through 264
    Processing sheet with id=AB3, first strand: chain 'B' and resid 362 through 364
      removed outlier: 6.366A  pdb=" N   VAL B 330 " --> pdb=" O   LYS B 362 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   MET B 364 " --> pdb=" O   VAL B 330 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   GLN B 332 " --> pdb=" O   MET B 364 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   ILE B 303 " --> pdb=" O   GLU B 329 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   SER B 302 " --> pdb=" O   HIS B 393 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   VAL B 395 " --> pdb=" O   SER B 302 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   THR B 304 " --> pdb=" O   VAL B 395 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 369 through 375
      removed outlier: 3.514A  pdb=" N   SER B 371 " --> pdb=" O   LYS B 382 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 421 through 422
      removed outlier: 7.081A  pdb=" N   PHE B 421 " --> pdb=" O   CYS B 441 " (cutoff:3.500A)
      removed outlier: 8.304A  pdb=" N   TYR B 443 " --> pdb=" O   PHE B 421 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   PHE B 442 " --> pdb=" O   ARG B 450 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ARG B 450 " --> pdb=" O   PHE B 442 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'B' and resid 484 through 486
      removed outlier: 3.747A  pdb=" N   VAL B 490 " --> pdb=" O   LEU B 486 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE B 576 " --> pdb=" O   ILE B 495 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   TYR B 567 " --> pdb=" O   VAL B 574 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   ILE B 576 " --> pdb=" O   ILE B 565 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   ILE B 565 " --> pdb=" O   ILE B 576 " (cutoff:3.500A)
      removed outlier: 5.479A  pdb=" N   LEU B 578 " --> pdb=" O   GLY B 563 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   GLY B 563 " --> pdb=" O   LEU B 578 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   PHE B 566 " --> pdb=" O   VAL B 505 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL B 505 " --> pdb=" O   PHE B 566 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 45
      removed outlier: 3.701A  pdb=" N   LEU D  98 " --> pdb=" O   ALA D  18 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   VAL D  19 " --> pdb=" O   ILE D 126 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   PHE D 128 " --> pdb=" O   VAL D  19 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   LEU D  21 " --> pdb=" O   PHE D 128 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 143 through 144

    305 hydrogen bonds defined for protein.
    861 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: 1.65

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2957
        1.34 -     1.47: 1985
        1.47 -     1.59: 4140
        1.59 -     1.72: 22
        1.72 -     1.84: 58
  Bond restraints: 9162
  Sorted by residual:
  bond pdb=" O2A NAD B 701 "
       pdb=" PA  NAD B 701 "
    ideal  model  delta    sigma   weight residual
    1.491  1.610 -0.119 2.00e-02 2.50e+03 3.56e+01
  bond pdb=" O2A NAD A 701 "
       pdb=" PA  NAD A 701 "
    ideal  model  delta    sigma   weight residual
    1.491  1.609 -0.118 2.00e-02 2.50e+03 3.51e+01
  bond pdb=" O2A FAD A 702 "
       pdb=" PA  FAD A 702 "
    ideal  model  delta    sigma   weight residual
    1.494  1.611 -0.117 2.00e-02 2.50e+03 3.40e+01
  bond pdb=" O2A FAD B 702 "
       pdb=" PA  FAD B 702 "
    ideal  model  delta    sigma   weight residual
    1.494  1.610 -0.116 2.00e-02 2.50e+03 3.37e+01
  bond pdb=" O2P FAD B 702 "
       pdb=" P   FAD B 702 "
    ideal  model  delta    sigma   weight residual
    1.495  1.610 -0.115 2.00e-02 2.50e+03 3.30e+01
  ... (remaining 9157 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.55: 12333
        4.55 -     9.09: 62
        9.09 -    13.64: 13
       13.64 -    18.18: 8
       18.18 -    22.73: 2
  Bond angle restraints: 12418
  Sorted by residual:
  angle pdb=" P   FAD B 702 "
        pdb=" O3P FAD B 702 "
        pdb=" PA  FAD B 702 "
      ideal   model   delta    sigma   weight residual
     130.34  107.61   22.73 3.00e+00 1.11e-01 5.74e+01
  angle pdb=" P   FAD A 702 "
        pdb=" O3P FAD A 702 "
        pdb=" PA  FAD A 702 "
      ideal   model   delta    sigma   weight residual
     130.34  109.75   20.59 3.00e+00 1.11e-01 4.71e+01
  angle pdb=" PA  NAD A 701 "
        pdb=" O3  NAD A 701 "
        pdb=" PN  NAD A 701 "
      ideal   model   delta    sigma   weight residual
     126.50  108.82   17.68 3.00e+00 1.11e-01 3.47e+01
  angle pdb=" PA  NAD B 701 "
        pdb=" O3  NAD B 701 "
        pdb=" PN  NAD B 701 "
      ideal   model   delta    sigma   weight residual
     126.50  109.29   17.21 3.00e+00 1.11e-01 3.29e+01
  angle pdb=" C5' FAD A 702 "
        pdb=" O5' FAD A 702 "
        pdb=" P   FAD A 702 "
      ideal   model   delta    sigma   weight residual
     121.27  106.17   15.10 3.00e+00 1.11e-01 2.53e+01
  ... (remaining 12413 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 5055
       17.50 -    35.00: 431
       35.00 -    52.50: 117
       52.50 -    70.00: 24
       70.00 -    87.49: 8
  Dihedral angle restraints: 5635
    sinusoidal: 2419
      harmonic: 3216
  Sorted by residual:
  dihedral pdb=" CB  CYS D  42 "
           pdb=" SG  CYS D  42 "
           pdb=" SG  CYS D  92 "
           pdb=" CB  CYS D  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -6.93  -79.07     1      1.00e+01 1.00e-02 7.78e+01
  dihedral pdb=" CA  ASP B 600 "
           pdb=" CB  ASP B 600 "
           pdb=" CG  ASP B 600 "
           pdb=" OD1 ASP B 600 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.00   57.00     1      2.00e+01 2.50e-03 1.09e+01
  dihedral pdb=" CB  MET D  53 "
           pdb=" CG  MET D  53 "
           pdb=" SD  MET D  53 "
           pdb=" CE  MET D  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.15  -58.85     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 5632 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1102
       0.056 -    0.112: 222
       0.112 -    0.169: 30
       0.169 -    0.225: 13
       0.225 -    0.281: 7
  Chirality restraints: 1374
  Sorted by residual:
  chirality pdb=" C1B NAD A 701 "
            pdb=" C2B NAD A 701 "
            pdb=" N9A NAD A 701 "
            pdb=" O4B NAD A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.63   -0.28 2.00e-01 2.50e+01 1.97e+00
  chirality pdb=" C1B FAD A 702 "
            pdb=" C2B FAD A 702 "
            pdb=" N9A FAD A 702 "
            pdb=" O4B FAD A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.61   -0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" C4D NAD B 701 "
            pdb=" C3D NAD B 701 "
            pdb=" C5D NAD B 701 "
            pdb=" O4D NAD B 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.74    0.26 2.00e-01 2.50e+01 1.69e+00
  ... (remaining 1371 not shown)

  Planarity restraints: 1582
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 172 "   -0.031 5.00e-02 4.00e+02   4.62e-02 3.41e+00
        pdb=" N   PRO B 173 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO B 173 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 173 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 173 "    0.025 5.00e-02 4.00e+02   3.77e-02 2.28e+00
        pdb=" N   PRO A 174 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 174 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 174 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 195 "    0.022 5.00e-02 4.00e+02   3.33e-02 1.77e+00
        pdb=" N   PRO D 196 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO D 196 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO D 196 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1579 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1253
        2.76 -     3.29: 8905
        3.29 -     3.83: 14900
        3.83 -     4.36: 16464
        4.36 -     4.90: 27936
  Nonbonded interactions: 69458
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D 112 "
            pdb=" OH  TYR D 200 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O3' FAD A 702 "
            pdb=" O5' FAD A 702 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OG  SER A 302 "
            pdb=" OE2 GLU A 329 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   LEU D  64 "
            pdb=" OG1 THR D  67 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" NE  ARG B 265 "
            pdb=" OE2 GLU B 401 "
     model   vdw
     2.278 3.120
  ... (remaining 69453 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 128 through 512 or resid 549 or resid 552 or resid 557 thr \ 
ough 611 or resid 701 through 702))
  selection = (chain 'B' and (resid 128 through 514 or resid 557 through 702))
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.270
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     10.980
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
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      :  0.005   0.119   9163  Z= 0.296
  Angle     :  0.973  22.729  12420  Z= 0.429
  Chirality :  0.052   0.281   1374
  Planarity :  0.004   0.046   1582
  Dihedral  : 14.576  87.494   3570
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  0.53 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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 aren not related in a simple way.
  whole: -0.39 (0.25), residues: 1124
  helix:  0.67 (0.30), residues: 328
  sheet: -0.39 (0.36), residues: 220
  loop : -0.68 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 239 
 TYR   0.006   0.001   TYR D 190 
 PHE   0.009   0.001   PHE D 227 
 TRP   0.010   0.001   TRP B 434 
 HIS   0.002   0.001   HIS A 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 9162)
  covalent geometry    : angle       0.96881 (12418)
  SS BOND              : bond        0.00722 (    1)
  SS BOND              : angle       6.77128 (    2)
  hydrogen bonds       : bond        0.22016 (  302)
  hydrogen bonds       : angle       7.99983 (  861)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 157
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 ASP cc_start: 0.8357 (m-30) cc_final: 0.8031 (t0)
REVERT: A  284 PHE cc_start: 0.8455 (t80) cc_final: 0.8023 (t80)
REVERT: A  333 LEU cc_start: 0.9482 (pp) cc_final: 0.9054 (tt)
REVERT: A  364 MET cc_start: 0.8269 (tpt) cc_final: 0.7887 (tpt)
REVERT: A  456 ASP cc_start: 0.8487 (t0) cc_final: 0.8092 (t70)
REVERT: A  486 LEU cc_start: 0.9368 (mt) cc_final: 0.8609 (tp)
REVERT: A  492 TYR cc_start: 0.8865 (p90) cc_final: 0.8424 (p90)
REVERT: A  585 MET cc_start: 0.8217 (tmm) cc_final: 0.7913 (tmm)
REVERT: B  253 TYR cc_start: 0.8942 (p90) cc_final: 0.8680 (p90)
REVERT: B  255 LYS cc_start: 0.9474 (mptt) cc_final: 0.9251 (mmmt)
REVERT: B  340 MET cc_start: 0.8043 (mmt) cc_final: 0.7791 (mmt)
REVERT: B  364 MET cc_start: 0.8788 (mpp) cc_final: 0.8387 (mpp)
REVERT: B  481 MET cc_start: 0.8677 (ptt) cc_final: 0.8147 (ptp)
REVERT: B  567 TYR cc_start: 0.7901 (m-80) cc_final: 0.7616 (m-80)
REVERT: D   20 LEU cc_start: 0.8354 (tp) cc_final: 0.7926 (tp)
REVERT: D   21 LEU cc_start: 0.8918 (mt) cc_final: 0.8534 (mt)
  outliers start: 4
  outliers final: 2
  residues processed: 159
  average time/residue: 0.1060
  time to fit residues: 23.0073
Evaluate side-chains
  105 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    0.0020
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.4980
   chunk 106 optimal weight:   30.0000
   overall best weight:    0.8392

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

Flipped N/Q/H residues before XYZ refinement:
B 468 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.091089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.067627 restraints weight = 40070.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.069622 restraints weight = 23500.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.071178 restraints weight = 16292.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.072008 restraints weight = 12558.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 59)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.072811 restraints weight = 10592.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9163  Z= 0.124
  Angle     :  0.573   9.504  12420  Z= 0.292
  Chirality :  0.045   0.196   1374
  Planarity :  0.004   0.046   1582
  Dihedral  : 10.114  82.843   1431
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  5.24 %
    Favored  : 94.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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 aren not related in a simple way.
  whole: -0.46 (0.25), residues: 1124
  helix:  0.57 (0.29), residues: 335
  sheet: -0.30 (0.36), residues: 194
  loop : -0.76 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 151 
 TYR   0.024   0.002   TYR A 443 
 PHE   0.016   0.001   PHE B 508 
 TRP   0.008   0.001   TRP B 579 
 HIS   0.003   0.001   HIS A 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9162)
  covalent geometry    : angle       0.57115 (12418)
  SS BOND              : bond        0.00855 (    1)
  SS BOND              : angle       3.65331 (    2)
  hydrogen bonds       : bond        0.04444 (  302)
  hydrogen bonds       : angle       6.23553 (  861)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 132
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 ASP cc_start: 0.8358 (m-30) cc_final: 0.8152 (t0)
REVERT: A  301 LYS cc_start: 0.7674 (tptp) cc_final: 0.7283 (tppt)
REVERT: A  333 LEU cc_start: 0.9452 (pp) cc_final: 0.9108 (tt)
REVERT: A  364 MET cc_start: 0.8041 (tpt) cc_final: 0.7779 (tpt)
REVERT: A  424 ASN cc_start: 0.8889 (p0) cc_final: 0.8630 (p0)
REVERT: A  453 GLU cc_start: 0.8444 (pm20) cc_final: 0.8229 (mp0)
REVERT: A  456 ASP cc_start: 0.8101 (t0) cc_final: 0.7876 (t70)
REVERT: A  492 TYR cc_start: 0.8451 (p90) cc_final: 0.8017 (p90)
REVERT: B  364 MET cc_start: 0.8729 (mpp) cc_final: 0.8478 (mpp)
REVERT: B  481 MET cc_start: 0.8749 (ptt) cc_final: 0.8281 (ptp)
REVERT: D   20 LEU cc_start: 0.8353 (tp) cc_final: 0.7970 (tt)
REVERT: D   21 LEU cc_start: 0.8490 (mt) cc_final: 0.8076 (mt)
REVERT: D  191 HIS cc_start: 0.9458 (m90) cc_final: 0.8997 (m90)
REVERT: D  201 TYR cc_start: 0.9424 (m-10) cc_final: 0.9186 (m-10)
REVERT: D  220 PHE cc_start: 0.8997 (t80) cc_final: 0.8694 (t80)
  outliers start: 3
  outliers final: 2
  residues processed: 135
  average time/residue: 0.0945
  time to fit residues: 18.1421
Evaluate side-chains
  101 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 74 optimal weight:    0.0010
   chunk 46 optimal weight:    5.9990
   chunk 96 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 101 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 89 optimal weight:   20.0000
   chunk 47 optimal weight:    4.9990
   overall best weight:    2.9994

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

Flipped N/Q/H residues before XYZ refinement:
B 350 ASN
** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.087716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.064092 restraints weight = 40591.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.066001 restraints weight = 24454.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.067309 restraints weight = 17235.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.068235 restraints weight = 13591.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.068777 restraints weight = 11503.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   9163  Z= 0.224
  Angle     :  0.649   8.961  12420  Z= 0.329
  Chirality :  0.045   0.139   1374
  Planarity :  0.005   0.036   1582
  Dihedral  :  9.053  85.139   1431
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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 aren not related in a simple way.
  whole: -0.79 (0.24), residues: 1124
  helix:  0.26 (0.28), residues: 348
  sheet: -0.55 (0.36), residues: 189
  loop : -0.95 (0.24), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 118 
 TYR   0.023   0.002   TYR A 347 
 PHE   0.033   0.002   PHE D 227 
 TRP   0.009   0.001   TRP B 579 
 HIS   0.005   0.001   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 9162)
  covalent geometry    : angle       0.64775 (12418)
  SS BOND              : bond        0.00801 (    1)
  SS BOND              : angle       2.76998 (    2)
  hydrogen bonds       : bond        0.04487 (  302)
  hydrogen bonds       : angle       6.03903 (  861)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  301 LYS cc_start: 0.7513 (tptp) cc_final: 0.6986 (tppt)
REVERT: A  333 LEU cc_start: 0.9548 (pp) cc_final: 0.9209 (tt)
REVERT: A  364 MET cc_start: 0.7941 (tpt) cc_final: 0.7687 (tpt)
REVERT: A  456 ASP cc_start: 0.8241 (t0) cc_final: 0.8026 (t70)
REVERT: A  492 TYR cc_start: 0.8563 (p90) cc_final: 0.8236 (p90)
REVERT: B  364 MET cc_start: 0.8783 (mpp) cc_final: 0.8416 (mpp)
REVERT: B  385 ASP cc_start: 0.6757 (m-30) cc_final: 0.6538 (t0)
REVERT: B  481 MET cc_start: 0.8941 (ptt) cc_final: 0.8162 (pmm)
REVERT: D   20 LEU cc_start: 0.8378 (tp) cc_final: 0.7966 (tt)
REVERT: D   21 LEU cc_start: 0.8593 (mt) cc_final: 0.8021 (mt)
REVERT: D  191 HIS cc_start: 0.9469 (m90) cc_final: 0.8980 (m90)
REVERT: D  201 TYR cc_start: 0.9287 (m-10) cc_final: 0.9084 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1034
  time to fit residues: 16.7932
Evaluate side-chains
  80 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  31 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.087661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.063863 restraints weight = 41223.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.065713 restraints weight = 24887.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.066977 restraints weight = 17490.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.067785 restraints weight = 13727.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.068458 restraints weight = 11638.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9163  Z= 0.169
  Angle     :  0.592   6.824  12420  Z= 0.303
  Chirality :  0.045   0.138   1374
  Planarity :  0.004   0.034   1582
  Dihedral  :  8.819  84.396   1431
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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 aren not related in a simple way.
  whole: -0.88 (0.25), residues: 1124
  helix:  0.20 (0.28), residues: 350
  sheet: -0.83 (0.37), residues: 197
  loop : -0.93 (0.25), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 118 
 TYR   0.017   0.001   TYR A 347 
 PHE   0.032   0.002   PHE D 227 
 TRP   0.008   0.001   TRP B 434 
 HIS   0.004   0.001   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 9162)
  covalent geometry    : angle       0.59101 (12418)
  SS BOND              : bond        0.00685 (    1)
  SS BOND              : angle       2.18417 (    2)
  hydrogen bonds       : bond        0.03903 (  302)
  hydrogen bonds       : angle       5.80750 (  861)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 LEU cc_start: 0.9551 (pp) cc_final: 0.9199 (tt)
REVERT: A  364 MET cc_start: 0.7953 (tpt) cc_final: 0.7625 (tpt)
REVERT: A  492 TYR cc_start: 0.8561 (p90) cc_final: 0.8105 (p90)
REVERT: B  364 MET cc_start: 0.8660 (mpp) cc_final: 0.8366 (mpp)
REVERT: B  481 MET cc_start: 0.8768 (ptt) cc_final: 0.8089 (pmm)
REVERT: B  567 TYR cc_start: 0.7851 (m-10) cc_final: 0.7580 (m-80)
REVERT: D   20 LEU cc_start: 0.8398 (tp) cc_final: 0.7985 (tt)
REVERT: D   21 LEU cc_start: 0.8623 (mt) cc_final: 0.8012 (mt)
REVERT: D   78 MET cc_start: 0.6286 (tpt) cc_final: 0.6069 (tpp)
REVERT: D  191 HIS cc_start: 0.9483 (m90) cc_final: 0.8962 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0940
  time to fit residues: 15.1071
Evaluate side-chains
  79 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 84 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 103 optimal weight:    0.0670
   chunk 54 optimal weight:    0.0970
   chunk 15 optimal weight:    3.9990
   chunk 100 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   overall best weight:    2.0322

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

Flipped N/Q/H residues before XYZ refinement:
A 428 GLN
** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.088033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.064589 restraints weight = 40338.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.066463 restraints weight = 24131.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.067738 restraints weight = 17019.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.068697 restraints weight = 13377.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.069255 restraints weight = 11272.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9163  Z= 0.162
  Angle     :  0.591   7.180  12420  Z= 0.301
  Chirality :  0.044   0.163   1374
  Planarity :  0.004   0.033   1582
  Dihedral  :  8.581  84.832   1431
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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 aren not related in a simple way.
  whole: -0.89 (0.24), residues: 1124
  helix:  0.17 (0.28), residues: 347
  sheet: -0.67 (0.37), residues: 189
  loop : -0.98 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  34 
 TYR   0.024   0.002   TYR A 347 
 PHE   0.032   0.002   PHE D 227 
 TRP   0.010   0.001   TRP A 483 
 HIS   0.004   0.001   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 9162)
  covalent geometry    : angle       0.58793 (12418)
  SS BOND              : bond        0.00233 (    1)
  SS BOND              : angle       4.88076 (    2)
  hydrogen bonds       : bond        0.03819 (  302)
  hydrogen bonds       : angle       5.67128 (  861)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 LEU cc_start: 0.9521 (pp) cc_final: 0.9158 (tt)
REVERT: A  364 MET cc_start: 0.7952 (tpt) cc_final: 0.7617 (tpt)
REVERT: A  492 TYR cc_start: 0.8420 (p90) cc_final: 0.7923 (p90)
REVERT: A  493 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7090 (mm-30)
REVERT: B  364 MET cc_start: 0.8621 (mpp) cc_final: 0.8372 (mpp)
REVERT: B  481 MET cc_start: 0.8658 (ptt) cc_final: 0.8405 (ptp)
REVERT: D   20 LEU cc_start: 0.8396 (tp) cc_final: 0.8034 (tt)
REVERT: D   21 LEU cc_start: 0.8665 (mt) cc_final: 0.7988 (mt)
REVERT: D   78 MET cc_start: 0.6652 (tpt) cc_final: 0.6406 (tpp)
REVERT: D  191 HIS cc_start: 0.9487 (m90) cc_final: 0.8964 (m90)
REVERT: D  201 TYR cc_start: 0.9408 (m-80) cc_final: 0.9185 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.0865
  time to fit residues: 13.6730
Evaluate side-chains
  81 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 37 optimal weight:    0.2980
   chunk 22 optimal weight:    3.9990
   chunk 94 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0060
   chunk 90 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 103 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
B 454 HIS
B 597 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.089809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.066232 restraints weight = 41366.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.068222 restraints weight = 24515.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.069576 restraints weight = 17181.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 62)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.070610 restraints weight = 13355.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.071162 restraints weight = 11269.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9163  Z= 0.105
  Angle     :  0.543   6.649  12420  Z= 0.277
  Chirality :  0.044   0.159   1374
  Planarity :  0.004   0.035   1582
  Dihedral  :  8.314  86.806   1431
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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 aren not related in a simple way.
  whole: -0.78 (0.25), residues: 1124
  helix:  0.32 (0.28), residues: 351
  sheet: -0.65 (0.37), residues: 182
  loop : -0.94 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 172 
 TYR   0.011   0.001   TYR D 201 
 PHE   0.020   0.001   PHE D 220 
 TRP   0.007   0.001   TRP B 434 
 HIS   0.003   0.001   HIS D  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 9162)
  covalent geometry    : angle       0.54267 (12418)
  SS BOND              : bond        0.00867 (    1)
  SS BOND              : angle       2.20020 (    2)
  hydrogen bonds       : bond        0.03334 (  302)
  hydrogen bonds       : angle       5.38980 (  861)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 LEU cc_start: 0.9535 (pp) cc_final: 0.9089 (tt)
REVERT: A  347 TYR cc_start: 0.7841 (p90) cc_final: 0.7625 (p90)
REVERT: A  364 MET cc_start: 0.7935 (tpt) cc_final: 0.7550 (tpt)
REVERT: A  492 TYR cc_start: 0.8364 (p90) cc_final: 0.7848 (p90)
REVERT: A  493 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7304 (mm-30)
REVERT: B  364 MET cc_start: 0.8704 (mpp) cc_final: 0.8412 (mpp)
REVERT: B  456 ASP cc_start: 0.8475 (t0) cc_final: 0.7895 (t70)
REVERT: B  567 TYR cc_start: 0.7885 (m-10) cc_final: 0.7604 (m-80)
REVERT: D   20 LEU cc_start: 0.8429 (tp) cc_final: 0.8114 (tt)
REVERT: D   21 LEU cc_start: 0.8607 (mt) cc_final: 0.7920 (mt)
REVERT: D   35 LEU cc_start: 0.9072 (mt) cc_final: 0.8659 (mt)
REVERT: D  191 HIS cc_start: 0.9509 (m90) cc_final: 0.8974 (m90)
REVERT: D  201 TYR cc_start: 0.9447 (m-80) cc_final: 0.9229 (m-80)
REVERT: D  220 PHE cc_start: 0.8986 (t80) cc_final: 0.8249 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0924
  time to fit residues: 16.0151
Evaluate side-chains
  92 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 40 optimal weight:    7.9990
   chunk 57 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 65 optimal weight:    2.9990
   chunk 111 optimal weight:    0.6980
   chunk 83 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0770
   overall best weight:    0.9542

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.089273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.065915 restraints weight = 41165.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.067772 restraints weight = 24581.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.069029 restraints weight = 17173.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.069999 restraints weight = 13448.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.070667 restraints weight = 11257.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9163  Z= 0.112
  Angle     :  0.560  11.657  12420  Z= 0.284
  Chirality :  0.044   0.156   1374
  Planarity :  0.004   0.034   1582
  Dihedral  :  8.156  89.026   1431
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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 aren not related in a simple way.
  whole: -0.68 (0.24), residues: 1124
  helix:  0.37 (0.28), residues: 349
  sheet: -0.54 (0.37), residues: 187
  loop : -0.88 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 387 
 TYR   0.019   0.001   TYR B 476 
 PHE   0.016   0.001   PHE D 220 
 TRP   0.004   0.001   TRP B 483 
 HIS   0.004   0.001   HIS B 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9162)
  covalent geometry    : angle       0.55925 (12418)
  SS BOND              : bond        0.00495 (    1)
  SS BOND              : angle       1.72480 (    2)
  hydrogen bonds       : bond        0.03387 (  302)
  hydrogen bonds       : angle       5.39149 (  861)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 LEU cc_start: 0.9553 (pp) cc_final: 0.9085 (tt)
REVERT: A  364 MET cc_start: 0.7934 (tpt) cc_final: 0.7550 (tpt)
REVERT: A  433 ILE cc_start: 0.9194 (mm) cc_final: 0.8922 (mm)
REVERT: A  469 MET cc_start: 0.8362 (mmm) cc_final: 0.7882 (mmm)
REVERT: A  492 TYR cc_start: 0.8438 (p90) cc_final: 0.7901 (p90)
REVERT: A  493 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7456 (mm-30)
REVERT: B  364 MET cc_start: 0.8685 (mpp) cc_final: 0.8393 (mpp)
REVERT: B  456 ASP cc_start: 0.8539 (t0) cc_final: 0.8004 (t70)
REVERT: B  567 TYR cc_start: 0.7861 (m-10) cc_final: 0.7534 (m-80)
REVERT: D   20 LEU cc_start: 0.8561 (tp) cc_final: 0.8298 (tt)
REVERT: D   21 LEU cc_start: 0.8632 (mt) cc_final: 0.8009 (mt)
REVERT: D   35 LEU cc_start: 0.9164 (mt) cc_final: 0.8740 (mt)
REVERT: D  191 HIS cc_start: 0.9507 (m90) cc_final: 0.8958 (m90)
REVERT: D  201 TYR cc_start: 0.9427 (m-80) cc_final: 0.9224 (m-80)
REVERT: D  220 PHE cc_start: 0.8977 (t80) cc_final: 0.8223 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.0863
  time to fit residues: 14.9595
Evaluate side-chains
  90 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 104 optimal weight:    0.0670
   chunk 38 optimal weight:    0.5980
   chunk 59 optimal weight:    9.9990
   chunk 94 optimal weight:   10.0000
   chunk 75 optimal weight:    0.7980
   chunk 90 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 102 optimal weight:    7.9990
   chunk 35 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   overall best weight:    0.6520

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.090006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.066374 restraints weight = 40678.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.068366 restraints weight = 24119.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.069835 restraints weight = 16848.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.070737 restraints weight = 13135.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.071368 restraints weight = 11024.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.3029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9163  Z= 0.107
  Angle     :  0.570   8.963  12420  Z= 0.286
  Chirality :  0.045   0.159   1374
  Planarity :  0.004   0.034   1582
  Dihedral  :  7.993  89.449   1431
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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 aren not related in a simple way.
  whole: -0.63 (0.25), residues: 1124
  helix:  0.38 (0.28), residues: 347
  sheet: -0.44 (0.37), residues: 187
  loop : -0.84 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 106 
 TYR   0.026   0.001   TYR A 347 
 PHE   0.030   0.001   PHE D 227 
 TRP   0.019   0.001   TRP A 434 
 HIS   0.004   0.001   HIS D  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 9162)
  covalent geometry    : angle       0.56985 (12418)
  SS BOND              : bond        0.00449 (    1)
  SS BOND              : angle       1.96424 (    2)
  hydrogen bonds       : bond        0.03312 (  302)
  hydrogen bonds       : angle       5.33104 (  861)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 LEU cc_start: 0.9519 (pp) cc_final: 0.9126 (tt)
REVERT: A  364 MET cc_start: 0.7933 (tpt) cc_final: 0.7532 (tpt)
REVERT: A  424 ASN cc_start: 0.8831 (p0) cc_final: 0.8612 (p0)
REVERT: A  492 TYR cc_start: 0.8408 (p90) cc_final: 0.7855 (p90)
REVERT: A  493 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7340 (mm-30)
REVERT: B  456 ASP cc_start: 0.8493 (t0) cc_final: 0.7959 (t70)
REVERT: B  567 TYR cc_start: 0.7850 (m-10) cc_final: 0.7534 (m-80)
REVERT: D   12 TYR cc_start: 0.7927 (t80) cc_final: 0.7582 (t80)
REVERT: D   20 LEU cc_start: 0.8546 (tp) cc_final: 0.8273 (tt)
REVERT: D   21 LEU cc_start: 0.8613 (mt) cc_final: 0.7994 (mt)
REVERT: D   35 LEU cc_start: 0.9052 (mt) cc_final: 0.8651 (mt)
REVERT: D  191 HIS cc_start: 0.9493 (m90) cc_final: 0.8951 (m90)
REVERT: D  201 TYR cc_start: 0.9416 (m-80) cc_final: 0.9208 (m-80)
REVERT: D  220 PHE cc_start: 0.9004 (t80) cc_final: 0.8160 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0935
  time to fit residues: 16.2391
Evaluate side-chains
  88 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0370
   chunk 90 optimal weight:    7.9990
   chunk 93 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0870
   chunk 10 optimal weight:    0.2980
   chunk 3 optimal weight:    2.9990
   chunk 74 optimal weight:    8.9990
   chunk 110 optimal weight:    0.0980
   chunk 64 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    0.7038

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.090306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.066440 restraints weight = 40382.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.068383 restraints weight = 24148.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.069650 restraints weight = 16914.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.070631 restraints weight = 13236.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.071334 restraints weight = 11164.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.3157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9163  Z= 0.105
  Angle     :  0.569   9.461  12420  Z= 0.283
  Chirality :  0.044   0.152   1374
  Planarity :  0.004   0.034   1582
  Dihedral  :  7.848  87.062   1431
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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 aren not related in a simple way.
  whole: -0.60 (0.25), residues: 1124
  helix:  0.39 (0.29), residues: 341
  sheet: -0.29 (0.39), residues: 177
  loop : -0.85 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 106 
 TYR   0.024   0.001   TYR A 347 
 PHE   0.022   0.001   PHE A 144 
 TRP   0.018   0.001   TRP A 434 
 HIS   0.003   0.001   HIS D  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 9162)
  covalent geometry    : angle       0.56871 (12418)
  SS BOND              : bond        0.00214 (    1)
  SS BOND              : angle       1.04543 (    2)
  hydrogen bonds       : bond        0.03274 (  302)
  hydrogen bonds       : angle       5.24552 (  861)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 LEU cc_start: 0.9486 (pp) cc_final: 0.9156 (tt)
REVERT: A  364 MET cc_start: 0.7918 (tpt) cc_final: 0.7621 (tpt)
REVERT: A  424 ASN cc_start: 0.8833 (p0) cc_final: 0.8611 (p0)
REVERT: A  493 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7399 (mm-30)
REVERT: B  364 MET cc_start: 0.8668 (mpp) cc_final: 0.8359 (mpp)
REVERT: B  456 ASP cc_start: 0.8540 (t0) cc_final: 0.8001 (t70)
REVERT: B  481 MET cc_start: 0.8572 (ptp) cc_final: 0.8367 (ptp)
REVERT: B  567 TYR cc_start: 0.7864 (m-10) cc_final: 0.7532 (m-80)
REVERT: D   20 LEU cc_start: 0.8568 (tp) cc_final: 0.8286 (tt)
REVERT: D   21 LEU cc_start: 0.8509 (mt) cc_final: 0.7829 (mt)
REVERT: D   35 LEU cc_start: 0.9070 (mt) cc_final: 0.8859 (mt)
REVERT: D  191 HIS cc_start: 0.9487 (m90) cc_final: 0.8941 (m90)
REVERT: D  201 TYR cc_start: 0.9480 (m-80) cc_final: 0.9279 (m-80)
REVERT: D  220 PHE cc_start: 0.8992 (t80) cc_final: 0.8003 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0897
  time to fit residues: 15.6365
Evaluate side-chains
  90 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 105 optimal weight:    0.7980
   chunk 94 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   chunk 38 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 83 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   chunk 60 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 69 optimal weight:    8.9990
   chunk 68 optimal weight:    0.0670
   overall best weight:    0.8720

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.089984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.066010 restraints weight = 40735.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.068022 restraints weight = 24319.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.069480 restraints weight = 17046.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.070320 restraints weight = 13287.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.070968 restraints weight = 11251.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.3192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9163  Z= 0.108
  Angle     :  0.565   9.164  12420  Z= 0.286
  Chirality :  0.044   0.146   1374
  Planarity :  0.004   0.051   1582
  Dihedral  :  7.761  84.354   1431
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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 aren not related in a simple way.
  whole: -0.61 (0.25), residues: 1124
  helix:  0.35 (0.29), residues: 342
  sheet: -0.35 (0.37), residues: 190
  loop : -0.82 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 569 
 TYR   0.023   0.001   TYR A 347 
 PHE   0.034   0.002   PHE D 227 
 TRP   0.005   0.001   TRP A 434 
 HIS   0.004   0.001   HIS D  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 9162)
  covalent geometry    : angle       0.56497 (12418)
  SS BOND              : bond        0.00261 (    1)
  SS BOND              : angle       1.17097 (    2)
  hydrogen bonds       : bond        0.03274 (  302)
  hydrogen bonds       : angle       5.23346 (  861)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 CYS cc_start: 0.8194 (p) cc_final: 0.7853 (p)
REVERT: A  333 LEU cc_start: 0.9499 (pp) cc_final: 0.9164 (tt)
REVERT: A  364 MET cc_start: 0.8397 (tpt) cc_final: 0.7834 (tpt)
REVERT: A  424 ASN cc_start: 0.8850 (p0) cc_final: 0.8635 (p0)
REVERT: A  456 ASP cc_start: 0.7688 (t70) cc_final: 0.6962 (t70)
REVERT: B  364 MET cc_start: 0.8678 (mpp) cc_final: 0.8326 (mpp)
REVERT: B  456 ASP cc_start: 0.8592 (t0) cc_final: 0.8051 (t70)
REVERT: B  567 TYR cc_start: 0.7937 (m-10) cc_final: 0.7575 (m-80)
REVERT: D   20 LEU cc_start: 0.8560 (tp) cc_final: 0.8227 (tp)
REVERT: D   21 LEU cc_start: 0.8530 (mt) cc_final: 0.7834 (mt)
REVERT: D   35 LEU cc_start: 0.9152 (mt) cc_final: 0.8867 (mt)
REVERT: D  152 TYR cc_start: 0.6605 (m-80) cc_final: 0.6291 (m-80)
REVERT: D  191 HIS cc_start: 0.9496 (m90) cc_final: 0.8956 (m90)
REVERT: D  220 PHE cc_start: 0.8959 (t80) cc_final: 0.8093 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0860
  time to fit residues: 14.6374
Evaluate side-chains
  85 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 96 optimal weight:    6.9990
   chunk 83 optimal weight:    0.0040
   chunk 105 optimal weight:    9.9990
   chunk 106 optimal weight:    0.5980
   chunk 28 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0170
   chunk 79 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.7234

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.090268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.066302 restraints weight = 40805.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.068277 restraints weight = 24519.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.069751 restraints weight = 17271.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.070731 restraints weight = 13510.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.071296 restraints weight = 11378.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.3300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9163  Z= 0.107
  Angle     :  0.582   9.106  12420  Z= 0.292
  Chirality :  0.045   0.186   1374
  Planarity :  0.004   0.038   1582
  Dihedral  :  7.696  81.711   1431
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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 aren not related in a simple way.
  whole: -0.60 (0.24), residues: 1124
  helix:  0.32 (0.28), residues: 342
  sheet: -0.29 (0.38), residues: 190
  loop : -0.81 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 569 
 TYR   0.040   0.001   TYR D 201 
 PHE   0.028   0.001   PHE A 144 
 TRP   0.020   0.001   TRP A 434 
 HIS   0.004   0.001   HIS D  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 9162)
  covalent geometry    : angle       0.58193 (12418)
  SS BOND              : bond        0.00250 (    1)
  SS BOND              : angle       1.20262 (    2)
  hydrogen bonds       : bond        0.03216 (  302)
  hydrogen bonds       : angle       5.23649 (  861)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1734.49 seconds
wall clock time: 30 minutes 38.71 seconds (1838.71 seconds total)