Starting phenix.real_space_refine
on Sat Aug 23 02:16:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k4b_36882/08_2025/8k4b_36882.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k4b_36882/08_2025/8k4b_36882.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k4b_36882/08_2025/8k4b_36882.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k4b_36882/08_2025/8k4b_36882.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k4b_36882/08_2025/8k4b_36882.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k4b_36882/08_2025/8k4b_36882.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.029
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P       6      5.49       5
     S      28      5.16       5
     C    5732      2.51       5
     N    1462      2.21       5
     O    1688      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8918
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 563, 4427
          Classifications: {'peptide': 563}
          Link IDs: {'PTRANS': 12, 'TRANS': 550}
    Chain: "B"
      Number of atoms: 4427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 563, 4427
          Classifications: {'peptide': 563}
          Link IDs: {'PTRANS': 12, 'TRANS': 550}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' ZN': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' ZN': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.70, per 1000 atoms: 0.19
  Number of scatterers: 8918
  At special positions: 0
  Unit cell: (77.35, 90.61, 142.545, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      28     16.00
     P       6     15.00
     O    1688      8.00
     N    1462      7.00
     C    5732      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 263.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2124

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 4 sheets defined
      67.2% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 158 through 163
    Processing helix  chain 'A' and resid 168 through 195
      removed outlier: 4.394A  pdb=" N   VAL A 172 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU A 173 " --> pdb=" O   ALA A 169 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER A 186 " --> pdb=" O   ASN A 182 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   LEU A 189 " --> pdb=" O   GLY A 185 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   GLN A 190 " --> pdb=" O   SER A 186 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   SER A 191 " --> pdb=" O   TYR A 187 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE A 192 " --> pdb=" O   TYR A 188 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   THR A 195 " --> pdb=" O   SER A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 251
      removed outlier: 4.448A  pdb=" N   LEU A 218 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   GLN A 219 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   GLN A 220 " --> pdb=" O   TYR A 216 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   VAL A 232 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   ASP A 240 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   VAL A 241 " --> pdb=" O   LEU A 237 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   TYR A 245 " --> pdb=" O   VAL A 241 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ILE A 246 " --> pdb=" O   ILE A 242 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   HIS A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 260
      removed outlier: 3.906A  pdb=" N   PHE A 257 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 271
      removed outlier: 3.766A  pdb=" N   ARG A 268 " --> pdb=" O   GLU A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 292
      removed outlier: 4.431A  pdb=" N   ASP A 277 " --> pdb=" O   ASN A 273 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   ALA A 278 " --> pdb=" O   SER A 274 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   VAL A 290 " --> pdb=" O   ILE A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 304
      removed outlier: 3.716A  pdb=" N   LEU A 298 " --> pdb=" O   VAL A 294 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL A 299 " --> pdb=" O   ILE A 295 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ASN A 304 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 313
      removed outlier: 3.662A  pdb=" N   THR A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU A 313 " --> pdb=" O   PHE A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 323
      removed outlier: 3.758A  pdb=" N   TYR A 318 " --> pdb=" O   ALA A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 353
      removed outlier: 4.698A  pdb=" N   GLU A 330 " --> pdb=" O   MET A 326 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   LYS A 331 " --> pdb=" O   LYS A 327 " (cutoff:3.500A)
      removed outlier: 4.991A  pdb=" N   MET A 332 " --> pdb=" O   PRO A 328 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   ASP A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   MET A 337 " --> pdb=" O   ASN A 333 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   GLU A 338 " --> pdb=" O   ARG A 334 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   GLY A 353 " --> pdb=" O   GLU A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 361
      removed outlier: 4.137A  pdb=" N   ILE A 357 " --> pdb=" O   GLY A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 416
      removed outlier: 4.226A  pdb=" N   ARG A 366 " --> pdb=" O   SER A 362 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LYS A 369 " --> pdb=" O   GLN A 365 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   VAL A 412 " --> pdb=" O   TRP A 408 " (cutoff:3.500A)
      removed outlier: 4.984A  pdb=" N   LEU A 413 " --> pdb=" O   MET A 409 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   VAL A 414 " --> pdb=" O   GLY A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 443
      removed outlier: 3.929A  pdb=" N   TYR A 433 " --> pdb=" O   THR A 429 " (cutoff:3.500A)
      Proline residue:  A 437  - end of helix
    Processing helix  chain 'A' and resid 444 through 463
      removed outlier: 3.843A  pdb=" N   LEU A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   THR A 450 " --> pdb=" O   THR A 446 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   VAL A 461 " --> pdb=" O   ARG A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 532
    Processing helix  chain 'A' and resid 552 through 559
    Processing helix  chain 'A' and resid 573 through 579
      removed outlier: 3.573A  pdb=" N   ASN A 577 " --> pdb=" O   THR A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 598
    Processing helix  chain 'A' and resid 623 through 638
      removed outlier: 4.011A  pdb=" N   THR A 638 " --> pdb=" O   ARG A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 664
    Processing helix  chain 'A' and resid 677 through 684
      removed outlier: 4.233A  pdb=" N   ALA A 681 " --> pdb=" O   ARG A 677 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   ARG A 683 " --> pdb=" O   THR A 679 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   THR A 684 " --> pdb=" O   ILE A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 707
    Processing helix  chain 'A' and resid 709 through 716
    Processing helix  chain 'B' and resid 158 through 163
    Processing helix  chain 'B' and resid 168 through 195
      removed outlier: 4.409A  pdb=" N   VAL B 172 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER B 186 " --> pdb=" O   ASN B 182 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   LEU B 189 " --> pdb=" O   GLY B 185 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLN B 190 " --> pdb=" O   SER B 186 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   SER B 191 " --> pdb=" O   TYR B 187 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE B 192 " --> pdb=" O   TYR B 188 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ILE B 193 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   THR B 195 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 251
      removed outlier: 4.447A  pdb=" N   LEU B 218 " --> pdb=" O   ILE B 214 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   GLN B 219 " --> pdb=" O   VAL B 215 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   GLN B 220 " --> pdb=" O   TYR B 216 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   VAL B 232 " --> pdb=" O   TYR B 228 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   ASP B 240 " --> pdb=" O   ARG B 236 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   VAL B 241 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   TYR B 245 " --> pdb=" O   VAL B 241 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ILE B 246 " --> pdb=" O   ILE B 242 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   HIS B 251 " --> pdb=" O   LYS B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 260
      removed outlier: 3.905A  pdb=" N   PHE B 257 " --> pdb=" O   PRO B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 271
      removed outlier: 3.946A  pdb=" N   ARG B 268 " --> pdb=" O   GLU B 264 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   PHE B 269 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 292
      removed outlier: 4.067A  pdb=" N   ALA B 278 " --> pdb=" O   SER B 274 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   VAL B 290 " --> pdb=" O   ILE B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 304
      removed outlier: 3.718A  pdb=" N   LEU B 298 " --> pdb=" O   VAL B 294 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL B 299 " --> pdb=" O   ILE B 295 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ASN B 304 " --> pdb=" O   LEU B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 313
      removed outlier: 3.660A  pdb=" N   THR B 311 " --> pdb=" O   LEU B 307 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU B 313 " --> pdb=" O   PHE B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 323
      removed outlier: 3.719A  pdb=" N   TYR B 318 " --> pdb=" O   ALA B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 353
      removed outlier: 4.698A  pdb=" N   GLU B 330 " --> pdb=" O   MET B 326 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   LYS B 331 " --> pdb=" O   LYS B 327 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   MET B 332 " --> pdb=" O   PRO B 328 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   ASP B 335 " --> pdb=" O   LYS B 331 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   MET B 337 " --> pdb=" O   ASN B 333 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   GLU B 338 " --> pdb=" O   ARG B 334 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   GLY B 353 " --> pdb=" O   GLU B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 361
      removed outlier: 4.136A  pdb=" N   ILE B 357 " --> pdb=" O   GLY B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 416
      removed outlier: 4.228A  pdb=" N   ARG B 366 " --> pdb=" O   SER B 362 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LYS B 369 " --> pdb=" O   GLN B 365 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   VAL B 412 " --> pdb=" O   TRP B 408 " (cutoff:3.500A)
      removed outlier: 4.984A  pdb=" N   LEU B 413 " --> pdb=" O   MET B 409 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   VAL B 414 " --> pdb=" O   GLY B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 420 through 443
      removed outlier: 3.842A  pdb=" N   TYR B 433 " --> pdb=" O   THR B 429 " (cutoff:3.500A)
      Proline residue:  B 437  - end of helix
    Processing helix  chain 'B' and resid 444 through 463
      removed outlier: 3.842A  pdb=" N   LEU B 448 " --> pdb=" O   LEU B 444 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   THR B 450 " --> pdb=" O   THR B 446 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   VAL B 461 " --> pdb=" O   ARG B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 522 through 532
    Processing helix  chain 'B' and resid 552 through 559
    Processing helix  chain 'B' and resid 573 through 579
      removed outlier: 3.567A  pdb=" N   ASN B 577 " --> pdb=" O   THR B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 588 through 598
    Processing helix  chain 'B' and resid 623 through 638
      removed outlier: 4.011A  pdb=" N   THR B 638 " --> pdb=" O   ARG B 634 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 653 through 664
    Processing helix  chain 'B' and resid 677 through 684
      removed outlier: 4.231A  pdb=" N   ALA B 681 " --> pdb=" O   ARG B 677 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ARG B 683 " --> pdb=" O   THR B 679 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   THR B 684 " --> pdb=" O   ILE B 680 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 700 through 707
    Processing helix  chain 'B' and resid 709 through 716
    Processing sheet with id=AA1, first strand: chain 'A' and resid 500 through 503
      removed outlier: 6.124A  pdb=" N   SER A 501 " --> pdb=" O   TYR A 491 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   TYR A 491 " --> pdb=" O   SER A 501 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   PHE A 486 " --> pdb=" O   SER A 542 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   SER A 542 " --> pdb=" O   PHE A 486 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   GLN A 488 " --> pdb=" O   GLU A 540 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   GLU A 540 " --> pdb=" O   GLN A 488 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 560 through 561
      removed outlier: 6.291A  pdb=" N   ASN A 561 " --> pdb=" O   ILE A 644 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ILE A 672 " --> pdb=" O   ILE A 643 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   VAL A 513 " --> pdb=" O   PHE A 673 " (cutoff:3.500A)
      removed outlier: 7.600A  pdb=" N   ALA A 675 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   PHE A 515 " --> pdb=" O   ALA A 675 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LYS A 686 " --> pdb=" O   LYS A 512 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   VAL A 688 " --> pdb=" O   ALA A 514 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   VAL A 687 " --> pdb=" O   GLU A 698 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   GLU A 698 " --> pdb=" O   VAL A 687 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   VAL A 689 " --> pdb=" O   VAL A 696 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 500 through 503
      removed outlier: 6.125A  pdb=" N   SER B 501 " --> pdb=" O   TYR B 491 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   TYR B 491 " --> pdb=" O   SER B 501 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   PHE B 486 " --> pdb=" O   SER B 542 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   SER B 542 " --> pdb=" O   PHE B 486 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   GLN B 488 " --> pdb=" O   GLU B 540 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   GLU B 540 " --> pdb=" O   GLN B 488 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 560 through 561
      removed outlier: 6.291A  pdb=" N   ASN B 561 " --> pdb=" O   ILE B 644 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ILE B 672 " --> pdb=" O   ILE B 643 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   VAL B 513 " --> pdb=" O   PHE B 673 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   ALA B 675 " --> pdb=" O   VAL B 513 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   PHE B 515 " --> pdb=" O   ALA B 675 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   LYS B 512 " --> pdb=" O   LYS B 686 " (cutoff:3.500A)
      removed outlier: 8.411A  pdb=" N   VAL B 688 " --> pdb=" O   LYS B 512 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   ALA B 514 " --> pdb=" O   VAL B 688 " (cutoff:3.500A)
      removed outlier: 7.972A  pdb=" N   LEU B 690 " --> pdb=" O   ALA B 514 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   VAL B 516 " --> pdb=" O   LEU B 690 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   VAL B 687 " --> pdb=" O   GLU B 698 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   GLU B 698 " --> pdb=" O   VAL B 687 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   VAL B 689 " --> pdb=" O   VAL B 696 " (cutoff:3.500A)

    481 hydrogen bonds defined for protein.
    1437 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: 1.05

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2788
        1.34 -     1.47: 1960
        1.47 -     1.59: 4236
        1.59 -     1.71: 10
        1.71 -     1.83: 56
  Bond restraints: 9050
  Sorted by residual:
  bond pdb=" C5  ATP B 801 "
       pdb=" C6  ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.409  1.308  0.101 1.00e-02 1.00e+04 1.02e+02
  bond pdb=" C5  ATP A 801 "
       pdb=" C6  ATP A 801 "
    ideal  model  delta    sigma   weight residual
    1.409  1.308  0.101 1.00e-02 1.00e+04 1.01e+02
  bond pdb=" C2  ATP A 801 "
       pdb=" N1  ATP A 801 "
    ideal  model  delta    sigma   weight residual
    1.334  1.420 -0.086 1.00e-02 1.00e+04 7.35e+01
  bond pdb=" C2  ATP B 801 "
       pdb=" N1  ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.334  1.419 -0.085 1.00e-02 1.00e+04 7.26e+01
  bond pdb=" C1' ATP A 801 "
       pdb=" C2' ATP A 801 "
    ideal  model  delta    sigma   weight residual
    1.531  1.434  0.097 1.20e-02 6.94e+03 6.54e+01
  ... (remaining 9045 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.28: 11809
        3.28 -     6.55: 381
        6.55 -     9.83: 73
        9.83 -    13.10: 13
       13.10 -    16.38: 2
  Bond angle restraints: 12278
  Sorted by residual:
  angle pdb=" PA  ATP B 801 "
        pdb=" O3A ATP B 801 "
        pdb=" PB  ATP B 801 "
      ideal   model   delta    sigma   weight residual
     136.83  120.45   16.38 1.00e+00 1.00e+00 2.68e+02
  angle pdb=" PA  ATP A 801 "
        pdb=" O3A ATP A 801 "
        pdb=" PB  ATP A 801 "
      ideal   model   delta    sigma   weight residual
     136.83  120.48   16.35 1.00e+00 1.00e+00 2.67e+02
  angle pdb=" N1  ATP A 801 "
        pdb=" C2  ATP A 801 "
        pdb=" N3  ATP A 801 "
      ideal   model   delta    sigma   weight residual
     128.69  117.41   11.28 1.00e+00 1.00e+00 1.27e+02
  angle pdb=" N1  ATP B 801 "
        pdb=" C2  ATP B 801 "
        pdb=" N3  ATP B 801 "
      ideal   model   delta    sigma   weight residual
     128.69  117.43   11.26 1.00e+00 1.00e+00 1.27e+02
  angle pdb=" PB  ATP B 801 "
        pdb=" O3B ATP B 801 "
        pdb=" PG  ATP B 801 "
      ideal   model   delta    sigma   weight residual
     139.87  129.76   10.11 1.00e+00 1.00e+00 1.02e+02
  ... (remaining 12273 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 4874
       17.62 -    35.23: 492
       35.23 -    52.85: 115
       52.85 -    70.46: 23
       70.46 -    88.08: 14
  Dihedral angle restraints: 5518
    sinusoidal: 2224
      harmonic: 3294
  Sorted by residual:
  dihedral pdb=" CA  ILE B 622 "
           pdb=" C   ILE B 622 "
           pdb=" N   SER B 623 "
           pdb=" CA  SER B 623 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.80  -28.20     0      5.00e+00 4.00e-02 3.18e+01
  dihedral pdb=" CA  ILE A 622 "
           pdb=" C   ILE A 622 "
           pdb=" N   SER A 623 "
           pdb=" CA  SER A 623 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.91  -28.09     0      5.00e+00 4.00e-02 3.16e+01
  dihedral pdb=" CA  ASP B 653 "
           pdb=" C   ASP B 653 "
           pdb=" N   ILE B 654 "
           pdb=" CA  ILE B 654 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.81  -20.19     0      5.00e+00 4.00e-02 1.63e+01
  ... (remaining 5515 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 1219
       0.075 -    0.150: 233
       0.150 -    0.225: 26
       0.225 -    0.300: 12
       0.300 -    0.375: 8
  Chirality restraints: 1498
  Sorted by residual:
  chirality pdb=" CB  ILE A 622 "
            pdb=" CA  ILE A 622 "
            pdb=" CG1 ILE A 622 "
            pdb=" CG2 ILE A 622 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.37 2.00e-01 2.50e+01 3.51e+00
  chirality pdb=" CB  ILE B 622 "
            pdb=" CA  ILE B 622 "
            pdb=" CG1 ILE B 622 "
            pdb=" CG2 ILE B 622 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.37 2.00e-01 2.50e+01 3.40e+00
  chirality pdb=" CB  VAL B 531 "
            pdb=" CA  VAL B 531 "
            pdb=" CG1 VAL B 531 "
            pdb=" CG2 VAL B 531 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.27   -0.36 2.00e-01 2.50e+01 3.22e+00
  ... (remaining 1495 not shown)

  Planarity restraints: 1522
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 252 "   -0.064 5.00e-02 4.00e+02   9.80e-02 1.54e+01
        pdb=" N   PRO A 253 "    0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO A 253 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO A 253 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 252 "    0.064 5.00e-02 4.00e+02   9.72e-02 1.51e+01
        pdb=" N   PRO B 253 "   -0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO B 253 "    0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO B 253 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 614 "    0.015 2.00e-02 2.50e+03   2.99e-02 8.95e+00
        pdb=" CD  GLU A 614 "   -0.052 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 614 "    0.019 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 614 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1519 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 72
        2.59 -     3.17: 7257
        3.17 -     3.74: 14121
        3.74 -     4.32: 17989
        4.32 -     4.90: 28464
  Nonbonded interactions: 67903
  Sorted by model distance:
  nonbonded pdb=" O3G ATP B 801 "
            pdb="ZN    ZN B 802 "
     model   vdw
     2.010 2.230
  nonbonded pdb=" O3G ATP A 801 "
            pdb="ZN    ZN A 802 "
     model   vdw
     2.010 2.230
  nonbonded pdb=" O2B ATP A 801 "
            pdb="ZN    ZN A 802 "
     model   vdw
     2.072 2.230
  nonbonded pdb=" O2B ATP B 801 "
            pdb="ZN    ZN B 802 "
     model   vdw
     2.072 2.230
  nonbonded pdb=" OG  SER A 385 "
            pdb=" CD2 LEU B 231 "
     model   vdw
     2.265 3.460
  ... (remaining 67898 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.780
  Find NCS groups from input model:        0.180
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
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      :  0.007   0.101   9050  Z= 0.482
  Angle     :  1.397  16.379  12278  Z= 0.795
  Chirality :  0.067   0.375   1498
  Planarity :  0.008   0.098   1522
  Dihedral  : 15.605  88.080   3394
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.04 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  1.92 %
    Favored  : 97.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.82 (0.20), residues: 1122
  helix: -2.28 (0.15), residues: 710
  sheet: -0.52 (0.73), residues: 68
  loop : -3.15 (0.25), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 627 
 TYR   0.034   0.002   TYR B 188 
 PHE   0.022   0.002   PHE A 434 
 TRP   0.017   0.004   TRP A 408 
 HIS   0.003   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00713 ( 9050)
  covalent geometry    : angle       1.39673 (12278)
  hydrogen bonds       : bond        0.14521 (  481)
  hydrogen bonds       : angle       6.97656 ( 1437)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 255
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8531 (ppp) cc_final: 0.8172 (tmm)
REVERT: A  247 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8862 (tptt)
REVERT: A  271 ASP cc_start: 0.8026 (t0) cc_final: 0.7665 (t70)
REVERT: A  310 MET cc_start: 0.8639 (pmm) cc_final: 0.8000 (mmt)
REVERT: A  312 LEU cc_start: 0.9177 (tp) cc_final: 0.8741 (pp)
REVERT: A  409 MET cc_start: 0.6014 (mmp) cc_final: 0.5774 (tmm)
REVERT: A  492 LYS cc_start: 0.8580 (tppt) cc_final: 0.8139 (mmtt)
REVERT: B  309 PHE cc_start: 0.5798 (t80) cc_final: 0.5391 (t80)
REVERT: B  561 ASN cc_start: 0.7874 (p0) cc_final: 0.7429 (m-40)
REVERT: B  690 LEU cc_start: 0.8382 (tp) cc_final: 0.7897 (tp)
  outliers start: 9
  outliers final: 1
  residues processed: 261
  average time/residue: 0.0838
  time to fit residues: 29.4582
Evaluate side-chains
  160 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 158
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 LYS
Chi-restraints excluded: chain B residue  219 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 455 ASN
A 456 ASN
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 455 ASN
B 550 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.108886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.083985 restraints weight = 30411.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.086652 restraints weight = 17404.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.088410 restraints weight = 11895.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.089603 restraints weight = 9212.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.090357 restraints weight = 7750.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9050  Z= 0.173
  Angle     :  0.759  13.632  12278  Z= 0.386
  Chirality :  0.042   0.183   1498
  Planarity :  0.006   0.075   1522
  Dihedral  :  8.575  80.827   1287
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 11.82 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.70 (0.24), residues: 1122
  helix: -0.45 (0.19), residues: 712
  sheet:  0.24 (0.94), residues: 46
  loop : -2.56 (0.27), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 260 
 TYR   0.019   0.002   TYR B 562 
 PHE   0.022   0.002   PHE B 434 
 TRP   0.009   0.002   TRP B 408 
 HIS   0.004   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 9050)
  covalent geometry    : angle       0.75917 (12278)
  hydrogen bonds       : bond        0.06030 (  481)
  hydrogen bonds       : angle       4.75622 ( 1437)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 164
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8895 (ppp) cc_final: 0.8669 (ppp)
REVERT: A  323 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7754 (t80)
REVERT: A  326 MET cc_start: 0.8073 (tmm) cc_final: 0.7347 (tmm)
REVERT: A  468 PHE cc_start: 0.8310 (m-10) cc_final: 0.8028 (m-80)
REVERT: B  254 MET cc_start: 0.8655 (tpt) cc_final: 0.8215 (tpp)
REVERT: B  326 MET cc_start: 0.7013 (tpt) cc_final: 0.6672 (tpt)
REVERT: B  395 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8543 (mtmt)
REVERT: B  455 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8707 (t0)
REVERT: B  503 ILE cc_start: 0.8880 (mm) cc_final: 0.8590 (mp)
REVERT: B  550 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8328 (tm-30)
REVERT: B  657 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8452 (mp0)
REVERT: B  690 LEU cc_start: 0.9050 (tp) cc_final: 0.8689 (tp)
REVERT: B  711 TYR cc_start: 0.8597 (t80) cc_final: 0.8233 (t80)
  outliers start: 40
  outliers final: 26
  residues processed: 184
  average time/residue: 0.0676
  time to fit residues: 17.6114
Evaluate side-chains
  173 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 143
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain B residue  219 GLN
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  250 PHE
Chi-restraints excluded: chain B residue  335 ASP
Chi-restraints excluded: chain B residue  346 SER
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  424 LEU
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  455 ASN
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  644 ILE
Chi-restraints excluded: chain B residue  657 GLU
Chi-restraints excluded: chain B residue  684 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 33 optimal weight:    8.9990
   chunk 62 optimal weight:    9.9990
   chunk 59 optimal weight:    3.9990
   chunk 39 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   chunk 101 optimal weight:    4.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 HIS
B 219 GLN
B 352 ASN
B 550 GLN
B 566 GLN
** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 612 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.104682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.079926 restraints weight = 31173.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.082433 restraints weight = 17875.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.084126 restraints weight = 12326.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.085214 restraints weight = 9610.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.085937 restraints weight = 8191.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.4254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9050  Z= 0.194
  Angle     :  0.750   9.222  12278  Z= 0.380
  Chirality :  0.042   0.184   1498
  Planarity :  0.005   0.066   1522
  Dihedral  :  8.196  81.514   1283
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 16.06 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.18 (0.24), residues: 1122
  helix: -0.02 (0.19), residues: 712
  sheet:  0.15 (0.89), residues: 46
  loop : -2.34 (0.28), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 260 
 TYR   0.028   0.002   TYR A 216 
 PHE   0.029   0.002   PHE B 308 
 TRP   0.007   0.001   TRP A 408 
 HIS   0.004   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 9050)
  covalent geometry    : angle       0.74950 (12278)
  hydrogen bonds       : bond        0.06161 (  481)
  hydrogen bonds       : angle       4.72481 ( 1437)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 158
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8983 (ppp) cc_final: 0.7947 (ppp)
REVERT: A  312 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8711 (pp)
REVERT: A  326 MET cc_start: 0.8305 (tmm) cc_final: 0.7729 (tmm)
REVERT: A  431 LEU cc_start: 0.9565 (tp) cc_final: 0.9292 (tp)
REVERT: B  196 TYR cc_start: 0.5120 (t80) cc_final: 0.4022 (t80)
REVERT: B  254 MET cc_start: 0.8863 (tpt) cc_final: 0.8499 (tpp)
REVERT: B  291 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.8033 (p)
REVERT: B  310 MET cc_start: 0.8842 (ppp) cc_final: 0.8584 (ppp)
REVERT: B  326 MET cc_start: 0.7171 (tpt) cc_final: 0.6768 (tpp)
REVERT: B  395 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8690 (ttpt)
REVERT: B  503 ILE cc_start: 0.8863 (mm) cc_final: 0.8582 (mp)
REVERT: B  550 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8720 (tm-30)
REVERT: B  657 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8567 (mp0)
REVERT: B  690 LEU cc_start: 0.9058 (tp) cc_final: 0.8719 (tp)
REVERT: B  701 HIS cc_start: 0.9290 (OUTLIER) cc_final: 0.8619 (t70)
REVERT: B  711 TYR cc_start: 0.8667 (t80) cc_final: 0.8201 (t80)
  outliers start: 43
  outliers final: 33
  residues processed: 183
  average time/residue: 0.0660
  time to fit residues: 17.7620
Evaluate side-chains
  174 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 136
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  291 SER
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  346 SER
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  381 SER
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  424 LEU
Chi-restraints excluded: chain B residue  425 ILE
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  657 GLU
Chi-restraints excluded: chain B residue  684 THR
Chi-restraints excluded: chain B residue  701 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0570
   chunk 69 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 60 optimal weight:    0.0770
   chunk 45 optimal weight:    0.0470
   chunk 76 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 108 optimal weight:    3.9990
   overall best weight:    0.3956

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 HIS
A 456 ASN
B 550 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.108558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.083701 restraints weight = 30780.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.086474 restraints weight = 17158.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.088243 restraints weight = 11683.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.089328 restraints weight = 9113.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.089919 restraints weight = 7788.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.4313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9050  Z= 0.130
  Angle     :  0.698   9.053  12278  Z= 0.337
  Chirality :  0.040   0.192   1498
  Planarity :  0.004   0.059   1522
  Dihedral  :  7.451  79.525   1280
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 20.30 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.93 (0.25), residues: 1122
  helix:  0.21 (0.20), residues: 722
  sheet:  0.45 (0.93), residues: 46
  loop : -2.44 (0.28), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 202 
 TYR   0.029   0.001   TYR A 216 
 PHE   0.022   0.001   PHE B 308 
 TRP   0.007   0.001   TRP B 408 
 HIS   0.003   0.001   HIS B 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9050)
  covalent geometry    : angle       0.69847 (12278)
  hydrogen bonds       : bond        0.05267 (  481)
  hydrogen bonds       : angle       4.24153 ( 1437)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 163
  time to evaluate  : 0.271 
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  201 MET cc_start: 0.8974 (ppp) cc_final: 0.7856 (ppp)
REVERT: A  265 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6822 (pt)
REVERT: A  312 LEU cc_start: 0.9196 (tt) cc_final: 0.8740 (pp)
REVERT: A  323 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7791 (t80)
REVERT: A  326 MET cc_start: 0.8144 (tmm) cc_final: 0.7551 (tmm)
REVERT: A  468 PHE cc_start: 0.8207 (m-10) cc_final: 0.7971 (m-80)
REVERT: B  196 TYR cc_start: 0.4935 (t80) cc_final: 0.4230 (t80)
REVERT: B  254 MET cc_start: 0.8655 (tpt) cc_final: 0.8399 (tpp)
REVERT: B  326 MET cc_start: 0.7272 (tpt) cc_final: 0.6746 (tpt)
REVERT: B  338 GLU cc_start: 0.8763 (tp30) cc_final: 0.8491 (tp30)
REVERT: B  407 LEU cc_start: 0.9541 (tp) cc_final: 0.9054 (pp)
REVERT: B  484 MET cc_start: 0.8416 (mmm) cc_final: 0.7875 (mmm)
REVERT: B  503 ILE cc_start: 0.8913 (mm) cc_final: 0.8637 (mp)
REVERT: B  550 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8560 (tm-30)
REVERT: B  690 LEU cc_start: 0.9031 (tp) cc_final: 0.8735 (tp)
REVERT: B  701 HIS cc_start: 0.9212 (OUTLIER) cc_final: 0.8601 (t-90)
REVERT: B  711 TYR cc_start: 0.8743 (t80) cc_final: 0.8402 (t80)
  outliers start: 36
  outliers final: 18
  residues processed: 185
  average time/residue: 0.0631
  time to fit residues: 16.7686
Evaluate side-chains
  162 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  424 LEU
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  593 ARG
Chi-restraints excluded: chain B residue  657 GLU
Chi-restraints excluded: chain B residue  701 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 48 optimal weight:    0.3980
   chunk 58 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 78 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 24 optimal weight:    0.2980
   chunk 95 optimal weight:    5.9990
   chunk 109 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 91 optimal weight:    4.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 HIS
B 550 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.108180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.083598 restraints weight = 30385.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.086312 restraints weight = 16978.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.088124 restraints weight = 11555.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.089286 restraints weight = 8922.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.090071 restraints weight = 7554.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.4563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9050  Z= 0.126
  Angle     :  0.705   8.282  12278  Z= 0.340
  Chirality :  0.041   0.272   1498
  Planarity :  0.004   0.054   1522
  Dihedral  :  7.189  83.897   1280
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 22.22 %
    Favored  : 75.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.72 (0.25), residues: 1122
  helix:  0.40 (0.20), residues: 712
  sheet:  0.42 (0.91), residues: 46
  loop : -2.34 (0.28), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 260 
 TYR   0.030   0.001   TYR A 216 
 PHE   0.027   0.001   PHE B 308 
 TRP   0.002   0.000   TRP B 408 
 HIS   0.003   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9050)
  covalent geometry    : angle       0.70478 (12278)
  hydrogen bonds       : bond        0.04998 (  481)
  hydrogen bonds       : angle       4.20552 ( 1437)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8967 (ppp) cc_final: 0.7758 (ppp)
REVERT: A  265 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6700 (pt)
REVERT: A  312 LEU cc_start: 0.9222 (tt) cc_final: 0.8767 (pp)
REVERT: A  323 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7804 (t80)
REVERT: A  326 MET cc_start: 0.8148 (tmm) cc_final: 0.7683 (tmm)
REVERT: A  468 PHE cc_start: 0.8150 (m-10) cc_final: 0.7943 (m-80)
REVERT: B  196 TYR cc_start: 0.4736 (t80) cc_final: 0.4074 (t80)
REVERT: B  326 MET cc_start: 0.7205 (tpt) cc_final: 0.6881 (tpt)
REVERT: B  338 GLU cc_start: 0.8721 (tp30) cc_final: 0.8404 (tp30)
REVERT: B  407 LEU cc_start: 0.9522 (tp) cc_final: 0.9053 (pp)
REVERT: B  431 LEU cc_start: 0.8510 (mt) cc_final: 0.8202 (mt)
REVERT: B  503 ILE cc_start: 0.8835 (mm) cc_final: 0.8565 (mp)
REVERT: B  550 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8579 (tm-30)
REVERT: B  607 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7558 (mtt)
REVERT: B  690 LEU cc_start: 0.9032 (tp) cc_final: 0.8753 (tp)
  outliers start: 26
  outliers final: 15
  residues processed: 163
  average time/residue: 0.0620
  time to fit residues: 14.6240
Evaluate side-chains
  156 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  607 MET
Chi-restraints excluded: chain B residue  653 ASP
Chi-restraints excluded: chain B residue  657 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 47 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    6.9990
   chunk 64 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 550 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.108315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.083539 restraints weight = 30793.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.086277 restraints weight = 17350.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.088077 restraints weight = 11842.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.089235 restraints weight = 9193.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.089789 restraints weight = 7817.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.4763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9050  Z= 0.126
  Angle     :  0.691   8.671  12278  Z= 0.335
  Chirality :  0.040   0.210   1498
  Planarity :  0.004   0.052   1522
  Dihedral  :  6.973  88.283   1280
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 23.23 %
    Favored  : 73.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.63 (0.25), residues: 1122
  helix:  0.46 (0.20), residues: 712
  sheet:  0.44 (0.91), residues: 46
  loop : -2.29 (0.28), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 260 
 TYR   0.031   0.001   TYR A 216 
 PHE   0.027   0.001   PHE B 308 
 TRP   0.001   0.000   TRP B 408 
 HIS   0.003   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9050)
  covalent geometry    : angle       0.69057 (12278)
  hydrogen bonds       : bond        0.04900 (  481)
  hydrogen bonds       : angle       4.17572 ( 1437)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 148
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8887 (ppp) cc_final: 0.7563 (ppp)
REVERT: A  265 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6789 (pt)
REVERT: A  323 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7865 (t80)
REVERT: A  392 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8767 (tmtt)
REVERT: A  495 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.6601 (m-80)
REVERT: B  326 MET cc_start: 0.7463 (tpt) cc_final: 0.6746 (tpt)
REVERT: B  338 GLU cc_start: 0.8769 (tp30) cc_final: 0.8451 (tp30)
REVERT: B  431 LEU cc_start: 0.8488 (mt) cc_final: 0.8277 (mt)
REVERT: B  503 ILE cc_start: 0.8851 (mm) cc_final: 0.8593 (mp)
REVERT: B  550 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8445 (tm-30)
REVERT: B  551 ILE cc_start: 0.8744 (mt) cc_final: 0.8257 (mm)
REVERT: B  678 LEU cc_start: 0.8830 (tp) cc_final: 0.8514 (tp)
REVERT: B  690 LEU cc_start: 0.9085 (tp) cc_final: 0.8811 (tp)
  outliers start: 33
  outliers final: 20
  residues processed: 167
  average time/residue: 0.0651
  time to fit residues: 15.6971
Evaluate side-chains
  162 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 137
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  657 GLU
Chi-restraints excluded: chain B residue  684 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 106 optimal weight:    0.8980
   chunk 111 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 89 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 550 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.108701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.084009 restraints weight = 31059.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.086762 restraints weight = 17593.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.088570 restraints weight = 12027.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.089695 restraints weight = 9324.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.090218 restraints weight = 7938.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.4958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9050  Z= 0.124
  Angle     :  0.698  10.954  12278  Z= 0.334
  Chirality :  0.040   0.190   1498
  Planarity :  0.004   0.050   1522
  Dihedral  :  6.810  87.811   1280
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 24.65 %
    Favored  : 72.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.62 (0.25), residues: 1122
  helix:  0.46 (0.20), residues: 718
  sheet:  0.53 (0.93), residues: 46
  loop : -2.31 (0.28), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 593 
 TYR   0.033   0.001   TYR A 216 
 PHE   0.025   0.001   PHE B 308 
 TRP   0.006   0.001   TRP B 408 
 HIS   0.004   0.001   HIS B 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 9050)
  covalent geometry    : angle       0.69777 (12278)
  hydrogen bonds       : bond        0.04836 (  481)
  hydrogen bonds       : angle       4.16040 ( 1437)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 143
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8870 (ppp) cc_final: 0.7488 (ppp)
REVERT: A  265 ILE cc_start: 0.7226 (OUTLIER) cc_final: 0.6882 (pt)
REVERT: A  312 LEU cc_start: 0.9325 (tt) cc_final: 0.8884 (pp)
REVERT: A  323 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7901 (t80)
REVERT: A  392 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8798 (tmtt)
REVERT: A  495 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.6417 (m-80)
REVERT: B  196 TYR cc_start: 0.4865 (t80) cc_final: 0.4538 (t80)
REVERT: B  326 MET cc_start: 0.7324 (tpt) cc_final: 0.6837 (tpt)
REVERT: B  338 GLU cc_start: 0.8709 (tp30) cc_final: 0.8383 (tp30)
REVERT: B  407 LEU cc_start: 0.9504 (tp) cc_final: 0.9025 (pp)
REVERT: B  503 ILE cc_start: 0.8819 (mm) cc_final: 0.8562 (mp)
REVERT: B  550 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8494 (tm-30)
REVERT: B  551 ILE cc_start: 0.8635 (mt) cc_final: 0.8125 (mm)
REVERT: B  690 LEU cc_start: 0.9082 (tp) cc_final: 0.8825 (tp)
  outliers start: 30
  outliers final: 20
  residues processed: 160
  average time/residue: 0.0625
  time to fit residues: 14.6537
Evaluate side-chains
  157 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  495 TYR
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  657 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 84 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 88 optimal weight:   20.0000
   chunk 46 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0170
   chunk 6 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.7218

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 550 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.108714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.084133 restraints weight = 30864.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.086891 restraints weight = 17358.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.088709 restraints weight = 11798.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.089859 restraints weight = 9145.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.090479 restraints weight = 7786.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.5066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9050  Z= 0.124
  Angle     :  0.720  12.498  12278  Z= 0.340
  Chirality :  0.041   0.239   1498
  Planarity :  0.004   0.048   1522
  Dihedral  :  6.679  87.213   1280
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 25.05 %
    Favored  : 71.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.25), residues: 1122
  helix:  0.51 (0.20), residues: 714
  sheet:  0.49 (0.93), residues: 46
  loop : -2.21 (0.28), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 593 
 TYR   0.032   0.001   TYR A 216 
 PHE   0.020   0.001   PHE B 434 
 TRP   0.001   0.000   TRP B 408 
 HIS   0.003   0.001   HIS B 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9050)
  covalent geometry    : angle       0.72019 (12278)
  hydrogen bonds       : bond        0.04775 (  481)
  hydrogen bonds       : angle       4.18051 ( 1437)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 140
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8840 (ppp) cc_final: 0.7442 (ppp)
REVERT: A  265 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6843 (pt)
REVERT: A  312 LEU cc_start: 0.9359 (tt) cc_final: 0.8919 (pp)
REVERT: A  323 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7937 (t80)
REVERT: A  326 MET cc_start: 0.8087 (tmm) cc_final: 0.7720 (tpp)
REVERT: A  392 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8810 (tmtt)
REVERT: A  409 MET cc_start: 0.6159 (mmp) cc_final: 0.5674 (tpp)
REVERT: A  495 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.6371 (m-80)
REVERT: B  196 TYR cc_start: 0.4897 (t80) cc_final: 0.4628 (t80)
REVERT: B  326 MET cc_start: 0.7419 (tpt) cc_final: 0.6887 (tpt)
REVERT: B  338 GLU cc_start: 0.8642 (tp30) cc_final: 0.8314 (tp30)
REVERT: B  407 LEU cc_start: 0.9511 (tp) cc_final: 0.9054 (pp)
REVERT: B  503 ILE cc_start: 0.8811 (mm) cc_final: 0.8559 (mp)
REVERT: B  550 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8539 (tm-30)
REVERT: B  551 ILE cc_start: 0.8604 (mt) cc_final: 0.8116 (mm)
REVERT: B  690 LEU cc_start: 0.9091 (tp) cc_final: 0.8831 (tp)
  outliers start: 30
  outliers final: 21
  residues processed: 158
  average time/residue: 0.0664
  time to fit residues: 15.1541
Evaluate side-chains
  159 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 133
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  308 PHE
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  495 TYR
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  657 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 78 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 26 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 550 GLN
B 676 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.108019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.083514 restraints weight = 31097.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.086202 restraints weight = 17700.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.087977 restraints weight = 12128.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.089122 restraints weight = 9433.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.089746 restraints weight = 8018.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.5235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9050  Z= 0.132
  Angle     :  0.729  11.349  12278  Z= 0.348
  Chirality :  0.042   0.199   1498
  Planarity :  0.004   0.076   1522
  Dihedral  :  6.651  86.310   1280
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 25.45 %
    Favored  : 71.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.25), residues: 1122
  helix:  0.51 (0.20), residues: 714
  sheet:  0.52 (0.94), residues: 46
  loop : -2.19 (0.29), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 593 
 TYR   0.031   0.001   TYR A 216 
 PHE   0.022   0.001   PHE B 434 
 TRP   0.001   0.000   TRP A 408 
 HIS   0.003   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 9050)
  covalent geometry    : angle       0.72932 (12278)
  hydrogen bonds       : bond        0.04918 (  481)
  hydrogen bonds       : angle       4.21703 ( 1437)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 136
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.7421 (ppp)
REVERT: A  265 ILE cc_start: 0.7191 (OUTLIER) cc_final: 0.6961 (pt)
REVERT: A  312 LEU cc_start: 0.9370 (tt) cc_final: 0.8925 (pp)
REVERT: A  323 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7969 (t80)
REVERT: A  326 MET cc_start: 0.8112 (tmm) cc_final: 0.7767 (tpp)
REVERT: A  392 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8801 (tmtt)
REVERT: A  409 MET cc_start: 0.6176 (mmp) cc_final: 0.5713 (tpp)
REVERT: A  495 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.6507 (m-80)
REVERT: B  196 TYR cc_start: 0.4921 (t80) cc_final: 0.4618 (t80)
REVERT: B  338 GLU cc_start: 0.8691 (tp30) cc_final: 0.8348 (tp30)
REVERT: B  407 LEU cc_start: 0.9555 (tp) cc_final: 0.9132 (pp)
REVERT: B  503 ILE cc_start: 0.8805 (mm) cc_final: 0.8536 (mp)
REVERT: B  550 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8578 (tm-30)
REVERT: B  551 ILE cc_start: 0.8721 (mt) cc_final: 0.8236 (mm)
REVERT: B  690 LEU cc_start: 0.9094 (tp) cc_final: 0.8846 (tp)
  outliers start: 30
  outliers final: 22
  residues processed: 154
  average time/residue: 0.0780
  time to fit residues: 17.7254
Evaluate side-chains
  160 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 132
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  201 MET
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  308 PHE
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  271 ASP
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  495 TYR
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  657 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 99 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    8.9990
   chunk 29 optimal weight:    3.9990
   chunk 96 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 81 optimal weight:   10.0000
   chunk 75 optimal weight:    2.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 550 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.105349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.080998 restraints weight = 32102.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.083641 restraints weight = 18001.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.085377 restraints weight = 12310.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.086439 restraints weight = 9547.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.087224 restraints weight = 8133.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.5522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9050  Z= 0.184
  Angle     :  0.781  11.463  12278  Z= 0.382
  Chirality :  0.043   0.201   1498
  Planarity :  0.005   0.059   1522
  Dihedral  :  6.832  82.819   1280
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 25.76 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.68 (0.25), residues: 1122
  helix:  0.36 (0.20), residues: 716
  sheet:  0.36 (0.92), residues: 46
  loop : -2.16 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 386 
 TYR   0.030   0.002   TYR A 216 
 PHE   0.026   0.002   PHE B 308 
 TRP   0.003   0.001   TRP A 408 
 HIS   0.004   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 9050)
  covalent geometry    : angle       0.78074 (12278)
  hydrogen bonds       : bond        0.05623 (  481)
  hydrogen bonds       : angle       4.52990 ( 1437)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 133
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.7475 (ppp)
REVERT: A  312 LEU cc_start: 0.9334 (tt) cc_final: 0.8873 (pp)
REVERT: A  326 MET cc_start: 0.8291 (tmm) cc_final: 0.7979 (tpp)
REVERT: A  495 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.6583 (m-80)
REVERT: B  196 TYR cc_start: 0.4960 (t80) cc_final: 0.4495 (t80)
REVERT: B  326 MET cc_start: 0.7045 (tpt) cc_final: 0.6722 (tpt)
REVERT: B  338 GLU cc_start: 0.8757 (tp30) cc_final: 0.8401 (tp30)
REVERT: B  350 ASP cc_start: 0.8547 (m-30) cc_final: 0.8227 (m-30)
REVERT: B  407 LEU cc_start: 0.9592 (tp) cc_final: 0.9179 (pp)
REVERT: B  503 ILE cc_start: 0.8837 (mm) cc_final: 0.8585 (mp)
REVERT: B  550 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8690 (tm-30)
REVERT: B  551 ILE cc_start: 0.8820 (mt) cc_final: 0.8398 (mm)
REVERT: B  657 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8438 (mp0)
REVERT: B  683 ARG cc_start: 0.8797 (mmm-85) cc_final: 0.8588 (mpt180)
REVERT: B  690 LEU cc_start: 0.9130 (tp) cc_final: 0.8907 (tp)
  outliers start: 32
  outliers final: 24
  residues processed: 153
  average time/residue: 0.0616
  time to fit residues: 13.7770
Evaluate side-chains
  157 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 129
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  201 MET
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  308 PHE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  346 SER
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  495 TYR
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  657 GLU
Chi-restraints excluded: chain B residue  684 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 109 optimal weight:    7.9990
   chunk 97 optimal weight:    0.0040
   chunk 46 optimal weight:    0.0010
   chunk 88 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0370
   chunk 111 optimal weight:    0.0470
   chunk 41 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.1974

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 550 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.110646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.086095 restraints weight = 31210.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.088869 restraints weight = 17641.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.090705 restraints weight = 12057.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.091860 restraints weight = 9343.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.092487 restraints weight = 7952.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.5532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9050  Z= 0.137
  Angle     :  0.774  14.320  12278  Z= 0.363
  Chirality :  0.043   0.228   1498
  Planarity :  0.004   0.048   1522
  Dihedral  :  6.579  81.387   1280
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 27.37 %
    Favored  : 69.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.25), residues: 1122
  helix:  0.53 (0.20), residues: 706
  sheet:  0.28 (0.91), residues: 46
  loop : -2.14 (0.28), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 260 
 TYR   0.028   0.001   TYR A 216 
 PHE   0.035   0.001   PHE B 308 
 TRP   0.002   0.000   TRP A 408 
 HIS   0.002   0.000   HIS B 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 9050)
  covalent geometry    : angle       0.77377 (12278)
  hydrogen bonds       : bond        0.04930 (  481)
  hydrogen bonds       : angle       4.29981 ( 1437)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1340.50 seconds
wall clock time: 23 minutes 53.80 seconds (1433.80 seconds total)