Starting phenix.real_space_refine
on Thu Jul  2 15:28:29 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8k4b_36882/07_2026/8k4b_36882.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k4b_36882/07_2026/8k4b_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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8k4b_36882/07_2026/8k4b_36882.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8k4b_36882/07_2026/8k4b_36882.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k4b_36882/07_2026/8k4b_36882.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k4b_36882/07_2026/8k4b_36882.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k4b_36882/07_2026/8k4b_36882.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k4b_36882/07_2026/8k4b_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 2.05, per 1000 atoms: 0.23
  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: 0.59
  Conformation dependent library (CDL) restraints added in 384.4 milliseconds
  

  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: 0.20
  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: 1.09

  Time building geometry restraints manager: 0.78 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 -    16.32: 4794
       16.32 -    32.64: 509
       32.64 -    48.97: 120
       48.97 -    65.29: 19
       65.29 -    81.61: 14
  Dihedral angle restraints: 5456
    sinusoidal: 2162
      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 5453 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:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.260
  Find NCS groups from input model:        0.090
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
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  : 14.770  81.610   3332
  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 are 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/Z
  covalent geometry    : bond        0.00713 /  0.48 ( 9050)
  covalent geometry    : angle       1.39673 /  0.79 (12278)
  hydrogen bonds       : bond        0.14521 /  9.91 (  481)
  hydrogen bonds       : angle       6.97656 /  4.88 ( 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  : 0.247 
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: 0.0855
  time to fit residues: 29.6696
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  : 0.336 
-------------------------------------------------------------------------------
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...
** 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 488 GLN
B 550 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.109049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.084099 restraints weight = 30420.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.086771 restraints weight = 17353.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.088529 restraints weight = 11869.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.089716 restraints weight = 9194.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.090342 restraints weight = 7764.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9050  Z= 0.174
  Angle     :  0.763  13.986  12278  Z= 0.387
  Chirality :  0.042   0.180   1498
  Planarity :  0.006   0.075   1522
  Dihedral  :  5.973  54.844   1225
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 12.32 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.73 (0.24), residues: 1122
  helix: -0.48 (0.19), residues: 712
  sheet:  0.25 (0.94), residues: 46
  loop : -2.56 (0.27), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 593 
 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   0.003   0.001   HIS A 490 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.17 ( 9050)
  covalent geometry    : angle       0.76340 /  0.39 (12278)
  hydrogen bonds       : bond        0.06081 /  4.03 (  481)
  hydrogen bonds       : angle       4.75744 /  3.30 ( 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
  202 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 165
  time to evaluate  : 0.269 
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: 0.8902 (ppp) cc_final: 0.8667 (ppp)
REVERT: A  323 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7699 (t80)
REVERT: A  326 MET cc_start: 0.8097 (tmm) cc_final: 0.7374 (tmm)
REVERT: A  468 PHE cc_start: 0.8267 (m-10) cc_final: 0.8015 (m-80)
REVERT: B  254 MET cc_start: 0.8659 (tpt) cc_final: 0.8235 (tpp)
REVERT: B  326 MET cc_start: 0.7009 (tpt) cc_final: 0.6668 (tpt)
REVERT: B  395 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8537 (mtmt)
REVERT: B  455 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8716 (t0)
REVERT: B  503 ILE cc_start: 0.8846 (mm) cc_final: 0.8558 (mp)
REVERT: B  550 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8231 (tm-30)
REVERT: B  551 ILE cc_start: 0.8354 (mm) cc_final: 0.8141 (mm)
REVERT: B  645 LEU cc_start: 0.7894 (mt) cc_final: 0.7606 (mp)
REVERT: B  657 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8440 (mp0)
REVERT: B  690 LEU cc_start: 0.9079 (tp) cc_final: 0.8741 (tp)
REVERT: B  711 TYR cc_start: 0.8609 (t80) cc_final: 0.8256 (t80)
  outliers start: 37
  outliers final: 26
  residues processed: 184
  average time/residue: 0.0728
  time to fit residues: 18.9737
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  : 0.381 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 62 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 39 optimal weight:    9.9990
   chunk 53 optimal weight:    6.9990
   chunk 101 optimal weight:    0.0980
   chunk 95 optimal weight:    8.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 HIS
A 456 ASN
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 550 GLN
** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.109455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.084366 restraints weight = 30289.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.087068 restraints weight = 17229.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.088901 restraints weight = 11811.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.090084 restraints weight = 9130.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.090859 restraints weight = 7714.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.3724

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= 0.133
  Angle     :  0.699   9.413  12278  Z= 0.345
  Chirality :  0.040   0.186   1498
  Planarity :  0.004   0.063   1522
  Dihedral  :  5.406  52.284   1221
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 15.76 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.25), residues: 1122
  helix:  0.03 (0.20), residues: 714
  sheet:  0.33 (0.93), residues: 46
  loop : -2.47 (0.27), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 260 
 TYR   0.029   0.001   TYR A 216 
 PHE   0.026   0.001   PHE B 308 
 TRP   0.007   0.001   TRP B 408 
 HIS   0.004   0.001   HIS A 490 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.13 ( 9050)
  covalent geometry    : angle       0.69899 /  0.34 (12278)
  hydrogen bonds       : bond        0.05444 /  3.63 (  481)
  hydrogen bonds       : angle       4.43228 /  3.08 ( 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
  183 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 153
  time to evaluate  : 0.261 
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: 0.8920 (ppp) cc_final: 0.8517 (ppp)
REVERT: A  323 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7694 (t80)
REVERT: A  326 MET cc_start: 0.8055 (tmm) cc_final: 0.7368 (tmm)
REVERT: A  431 LEU cc_start: 0.9553 (tp) cc_final: 0.9291 (tp)
REVERT: A  468 PHE cc_start: 0.8363 (m-10) cc_final: 0.8094 (m-80)
REVERT: A  607 MET cc_start: 0.7085 (mpp) cc_final: 0.6775 (mpp)
REVERT: A  627 ARG cc_start: 0.7960 (mmp80) cc_final: 0.7696 (mmp80)
REVERT: B  196 TYR cc_start: 0.5003 (t80) cc_final: 0.4189 (t80)
REVERT: B  201 MET cc_start: 0.9132 (mpp) cc_final: 0.8357 (mpp)
REVERT: B  254 MET cc_start: 0.8637 (tpt) cc_final: 0.8334 (tpp)
REVERT: B  271 ASP cc_start: 0.9111 (t0) cc_final: 0.8639 (p0)
REVERT: B  326 MET cc_start: 0.7260 (tpt) cc_final: 0.6553 (tpt)
REVERT: B  419 MET cc_start: 0.8087 (mmp) cc_final: 0.7871 (mmp)
REVERT: B  503 ILE cc_start: 0.8865 (mm) cc_final: 0.8578 (mp)
REVERT: B  550 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8531 (tm-30)
REVERT: B  645 LEU cc_start: 0.8052 (mt) cc_final: 0.7819 (mp)
REVERT: B  690 LEU cc_start: 0.9087 (tp) cc_final: 0.8756 (tp)
REVERT: B  701 HIS cc_start: 0.9281 (OUTLIER) cc_final: 0.8787 (t-90)
  outliers start: 30
  outliers final: 21
  residues processed: 171
  average time/residue: 0.0609
  time to fit residues: 15.1792
Evaluate side-chains
  163 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 139
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
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  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  432 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  559 TYR
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  402 LEU
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  461 VAL
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  657 GLU
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:    8.9990
   chunk 52 optimal weight:    5.9990
   chunk 64 optimal weight:    0.5980
   chunk 69 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 60 optimal weight:    0.2980
   chunk 45 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 108 optimal weight:    6.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 HIS
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 455 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 = 0.3885 r_free = 0.3885 target = 0.109931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.085098 restraints weight = 30814.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.087815 restraints weight = 17467.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.089598 restraints weight = 11998.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.090786 restraints weight = 9335.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.091510 restraints weight = 7931.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.4071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9050  Z= 0.122
  Angle     :  0.668   8.207  12278  Z= 0.326
  Chirality :  0.040   0.195   1498
  Planarity :  0.004   0.057   1522
  Dihedral  :  5.182  52.711   1221
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 17.58 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.25), residues: 1122
  helix:  0.26 (0.20), residues: 724
  sheet:  0.46 (0.93), residues: 46
  loop : -2.57 (0.27), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 260 
 TYR   0.030   0.001   TYR A 216 
 PHE   0.028   0.001   PHE B 308 
 TRP   0.009   0.001   TRP B 408 
 HIS   0.004   0.001   HIS B 713 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.12 ( 9050)
  covalent geometry    : angle       0.66837 /  0.33 (12278)
  hydrogen bonds       : bond        0.05038 /  3.34 (  481)
  hydrogen bonds       : angle       4.16040 /  2.89 ( 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
  200 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 159
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8943 (ppp) cc_final: 0.7833 (ppp)
REVERT: A  323 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7701 (t80)
REVERT: A  326 MET cc_start: 0.7998 (tmm) cc_final: 0.7374 (tmm)
REVERT: A  409 MET cc_start: 0.6393 (mmp) cc_final: 0.6087 (tpp)
REVERT: A  468 PHE cc_start: 0.8264 (m-10) cc_final: 0.8022 (m-80)
REVERT: A  607 MET cc_start: 0.6980 (mpp) cc_final: 0.6655 (mpp)
REVERT: A  622 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.7920 (pt)
REVERT: A  627 ARG cc_start: 0.7917 (mmp80) cc_final: 0.7485 (mmp80)
REVERT: B  196 TYR cc_start: 0.4845 (t80) cc_final: 0.4527 (t80)
REVERT: B  201 MET cc_start: 0.9120 (mpp) cc_final: 0.8683 (mpp)
REVERT: B  254 MET cc_start: 0.8639 (tpt) cc_final: 0.8384 (tpp)
REVERT: B  326 MET cc_start: 0.7214 (tpt) cc_final: 0.6772 (tpt)
REVERT: B  338 GLU cc_start: 0.8739 (tp30) cc_final: 0.8456 (tp30)
REVERT: B  407 LEU cc_start: 0.9471 (tp) cc_final: 0.9012 (pp)
REVERT: B  503 ILE cc_start: 0.8859 (mm) cc_final: 0.8590 (mp)
REVERT: B  550 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8614 (tm-30)
REVERT: B  645 LEU cc_start: 0.7966 (mt) cc_final: 0.7746 (mp)
REVERT: B  690 LEU cc_start: 0.8981 (tp) cc_final: 0.8664 (tp)
  outliers start: 41
  outliers final: 25
  residues processed: 183
  average time/residue: 0.0612
  time to fit residues: 16.0115
Evaluate side-chains
  165 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
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  218 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  250 PHE
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 A residue  622 ILE
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  219 GLN
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  250 PHE
Chi-restraints excluded: chain B residue  291 SER
Chi-restraints excluded: chain B residue  335 ASP
Chi-restraints excluded: chain B residue  346 SER
Chi-restraints excluded: chain B residue  381 SER
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  657 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 48 optimal weight:    0.2980
   chunk 58 optimal weight:    4.9990
   chunk 82 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 95 optimal weight:    0.7980
   chunk 109 optimal weight:    9.9990
   chunk 32 optimal weight:    0.0270
   chunk 91 optimal weight:    0.0270
   overall best weight:    0.4296

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 HIS
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 488 GLN
B 550 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.110847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.086118 restraints weight = 30306.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.088894 restraints weight = 16984.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.090673 restraints weight = 11638.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.091904 restraints weight = 9071.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.092691 restraints weight = 7706.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.4314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9050  Z= 0.120
  Angle     :  0.689   9.645  12278  Z= 0.331
  Chirality :  0.040   0.182   1498
  Planarity :  0.004   0.052   1522
  Dihedral  :  5.079  54.076   1221
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 20.10 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.25), residues: 1122
  helix:  0.40 (0.20), residues: 716
  sheet:  0.52 (0.93), residues: 46
  loop : -2.46 (0.27), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 260 
 TYR   0.030   0.001   TYR A 216 
 PHE   0.028   0.001   PHE B 308 
 TRP   0.006   0.001   TRP B 408 
 HIS   0.003   0.001   HIS A 490 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.12 ( 9050)
  covalent geometry    : angle       0.68930 /  0.33 (12278)
  hydrogen bonds       : bond        0.04723 /  3.14 (  481)
  hydrogen bonds       : angle       4.07768 /  2.82 ( 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
  193 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 159
  time to evaluate  : 0.293 
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: 0.8952 (ppp) cc_final: 0.7752 (ppp)
REVERT: A  265 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6589 (pt)
REVERT: A  312 LEU cc_start: 0.9236 (tt) cc_final: 0.8743 (pp)
REVERT: A  323 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7813 (t80)
REVERT: A  326 MET cc_start: 0.7979 (tmm) cc_final: 0.7384 (tmm)
REVERT: A  409 MET cc_start: 0.6190 (mmp) cc_final: 0.5791 (tpp)
REVERT: A  468 PHE cc_start: 0.8149 (m-10) cc_final: 0.7907 (m-80)
REVERT: A  622 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.7814 (pt)
REVERT: A  627 ARG cc_start: 0.7909 (mmp80) cc_final: 0.7582 (mmp80)
REVERT: B  201 MET cc_start: 0.9037 (mpp) cc_final: 0.8632 (mpp)
REVERT: B  326 MET cc_start: 0.7230 (tpt) cc_final: 0.6781 (tpt)
REVERT: B  338 GLU cc_start: 0.8702 (tp30) cc_final: 0.8392 (tp30)
REVERT: B  407 LEU cc_start: 0.9466 (tp) cc_final: 0.9018 (pp)
REVERT: B  413 LEU cc_start: 0.9101 (mm) cc_final: 0.8776 (pp)
REVERT: B  419 MET cc_start: 0.8017 (mmm) cc_final: 0.7568 (mmp)
REVERT: B  503 ILE cc_start: 0.8803 (mm) cc_final: 0.8533 (mp)
REVERT: B  550 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8646 (tm-30)
REVERT: B  645 LEU cc_start: 0.7937 (mt) cc_final: 0.7727 (mp)
REVERT: B  690 LEU cc_start: 0.9005 (tp) cc_final: 0.8700 (tp)
  outliers start: 34
  outliers final: 19
  residues processed: 180
  average time/residue: 0.0644
  time to fit residues: 16.9450
Evaluate side-chains
  165 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 142
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
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  218 LEU
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  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  563 LEU
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  219 GLN
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  250 PHE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  424 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
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:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 71 optimal weight:   20.0000
   chunk 98 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    0.0770
   chunk 64 optimal weight:    3.9990
   chunk 68 optimal weight:    0.8980
   chunk 66 optimal weight:    0.1980
   overall best weight:    0.5138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 550 GLN
B 565 GLN
B 612 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.110848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.086348 restraints weight = 30307.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.089114 restraints weight = 16988.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.090934 restraints weight = 11577.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.092138 restraints weight = 8978.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.092888 restraints weight = 7600.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.4591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9050  Z= 0.119
  Angle     :  0.678  10.708  12278  Z= 0.326
  Chirality :  0.040   0.183   1498
  Planarity :  0.004   0.050   1522
  Dihedral  :  5.016  55.120   1221
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 20.81 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.25), residues: 1122
  helix:  0.51 (0.20), residues: 710
  sheet:  0.54 (0.93), residues: 46
  loop : -2.42 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 593 
 TYR   0.030   0.001   TYR A 216 
 PHE   0.024   0.001   PHE B 308 
 TRP   0.005   0.001   TRP B 408 
 HIS   0.003   0.001   HIS A 490 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.12 ( 9050)
  covalent geometry    : angle       0.67820 /  0.33 (12278)
  hydrogen bonds       : bond        0.04633 /  3.08 (  481)
  hydrogen bonds       : angle       4.02430 /  2.78 ( 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
  184 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 149
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8816 (ppp) cc_final: 0.7518 (ppp)
REVERT: A  265 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6624 (pt)
REVERT: A  312 LEU cc_start: 0.9269 (tt) cc_final: 0.8756 (pp)
REVERT: A  323 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7816 (t80)
REVERT: A  326 MET cc_start: 0.7985 (tmm) cc_final: 0.7395 (tmm)
REVERT: A  392 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8876 (tmtt)
REVERT: A  409 MET cc_start: 0.5963 (mmp) cc_final: 0.5563 (tpp)
REVERT: A  468 PHE cc_start: 0.8182 (m-10) cc_final: 0.7946 (m-80)
REVERT: B  196 TYR cc_start: 0.5391 (t80) cc_final: 0.4887 (t80)
REVERT: B  271 ASP cc_start: 0.8912 (t0) cc_final: 0.8570 (p0)
REVERT: B  326 MET cc_start: 0.7292 (tpt) cc_final: 0.6735 (tpt)
REVERT: B  338 GLU cc_start: 0.8641 (tp30) cc_final: 0.8333 (tp30)
REVERT: B  407 LEU cc_start: 0.9456 (tp) cc_final: 0.9037 (pp)
REVERT: B  408 TRP cc_start: 0.5547 (t60) cc_final: 0.5228 (t60)
REVERT: B  413 LEU cc_start: 0.9071 (mm) cc_final: 0.8753 (pp)
REVERT: B  419 MET cc_start: 0.7998 (mmm) cc_final: 0.7571 (mmp)
REVERT: B  503 ILE cc_start: 0.8787 (mm) cc_final: 0.8518 (mp)
REVERT: B  550 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8547 (tm-30)
REVERT: B  678 LEU cc_start: 0.8751 (tp) cc_final: 0.8547 (tp)
REVERT: B  690 LEU cc_start: 0.9014 (tp) cc_final: 0.8664 (tp)
  outliers start: 35
  outliers final: 23
  residues processed: 173
  average time/residue: 0.0609
  time to fit residues: 15.5176
Evaluate side-chains
  170 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 143
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
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  218 LEU
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  559 TYR
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  219 GLN
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  250 PHE
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  495 TYR
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  653 ASP
Chi-restraints excluded: chain B residue  657 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 15 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9990
   chunk 111 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 89 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.9986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 219 GLN
B 550 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.109163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.084734 restraints weight = 30443.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.087476 restraints weight = 17130.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.089311 restraints weight = 11688.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.090415 restraints weight = 9042.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.091261 restraints weight = 7681.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.4770

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     :  0.690  10.201  12278  Z= 0.333
  Chirality :  0.040   0.266   1498
  Planarity :  0.004   0.047   1522
  Dihedral  :  5.054  56.059   1221
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 22.63 %
    Favored  : 73.84 %
  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 are not related in a simple way.
  whole: -0.61 (0.25), residues: 1122
  helix:  0.51 (0.20), residues: 714
  sheet:  0.37 (0.92), residues: 46
  loop : -2.37 (0.27), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 593 
 TYR   0.028   0.001   TYR A 216 
 PHE   0.026   0.001   PHE B 308 
 TRP   0.005   0.001   TRP B 408 
 HIS   0.003   0.001   HIS A 490 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 ( 9050)
  covalent geometry    : angle       0.68970 /  0.33 (12278)
  hydrogen bonds       : bond        0.04717 /  3.13 (  481)
  hydrogen bonds       : angle       4.06635 /  2.81 ( 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
  182 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 147
  time to evaluate  : 0.234 
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: 0.8824 (ppp) cc_final: 0.7489 (ppp)
REVERT: A  265 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6774 (pt)
REVERT: A  312 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8753 (pp)
REVERT: A  323 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7868 (t80)
REVERT: A  326 MET cc_start: 0.8084 (tmm) cc_final: 0.7480 (tmm)
REVERT: A  409 MET cc_start: 0.5936 (mmp) cc_final: 0.5533 (tpp)
REVERT: A  468 PHE cc_start: 0.8190 (m-10) cc_final: 0.7930 (m-80)
REVERT: A  495 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.6454 (m-80)
REVERT: B  201 MET cc_start: 0.8708 (mpp) cc_final: 0.8307 (mpp)
REVERT: B  271 ASP cc_start: 0.8880 (t0) cc_final: 0.8620 (p0)
REVERT: B  310 MET cc_start: 0.8457 (ppp) cc_final: 0.8232 (ppp)
REVERT: B  338 GLU cc_start: 0.8659 (tp30) cc_final: 0.8325 (tp30)
REVERT: B  407 LEU cc_start: 0.9476 (tp) cc_final: 0.9062 (pp)
REVERT: B  408 TRP cc_start: 0.5690 (t60) cc_final: 0.5316 (t60)
REVERT: B  413 LEU cc_start: 0.9095 (mm) cc_final: 0.8751 (pp)
REVERT: B  419 MET cc_start: 0.7993 (mmm) cc_final: 0.7554 (mmp)
REVERT: B  503 ILE cc_start: 0.8780 (mm) cc_final: 0.8518 (mp)
REVERT: B  550 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8655 (tm-30)
REVERT: B  690 LEU cc_start: 0.9067 (tp) cc_final: 0.8775 (tp)
  outliers start: 35
  outliers final: 27
  residues processed: 166
  average time/residue: 0.0628
  time to fit residues: 15.3575
Evaluate side-chains
  170 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 138
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
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  217 ILE
Chi-restraints excluded: chain A residue  218 LEU
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  312 LEU
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  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 B residue  195 THR
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  250 PHE
Chi-restraints excluded: chain B residue  291 SER
Chi-restraints excluded: chain B residue  346 SER
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  495 TYR
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  653 ASP
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:    5.9990
   chunk 84 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 88 optimal weight:    0.4980
   chunk 46 optimal weight:    0.0050
   chunk 27 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 39 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.8396

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 445 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 = 0.3891 r_free = 0.3891 target = 0.110158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.085495 restraints weight = 30514.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.088214 restraints weight = 17205.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.090052 restraints weight = 11828.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.091223 restraints weight = 9185.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.091957 restraints weight = 7804.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.4910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9050  Z= 0.125
  Angle     :  0.706   9.807  12278  Z= 0.338
  Chirality :  0.041   0.228   1498
  Planarity :  0.004   0.047   1522
  Dihedral  :  4.930  56.431   1218
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 23.43 %
    Favored  : 73.03 %
  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 are not related in a simple way.
  whole: -0.56 (0.25), residues: 1122
  helix:  0.55 (0.20), residues: 710
  sheet:  0.34 (0.91), residues: 46
  loop : -2.30 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 593 
 TYR   0.028   0.001   TYR A 216 
 PHE   0.024   0.001   PHE B 308 
 TRP   0.006   0.001   TRP B 408 
 HIS   0.003   0.001   HIS A 490 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 ( 9050)
  covalent geometry    : angle       0.70636 /  0.34 (12278)
  hydrogen bonds       : bond        0.04730 /  3.15 (  481)
  hydrogen bonds       : angle       4.06765 /  2.82 ( 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
  178 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 143
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8785 (ppp) cc_final: 0.7387 (ppp)
REVERT: A  265 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6750 (pt)
REVERT: A  312 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8749 (pp)
REVERT: A  323 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7931 (t80)
REVERT: A  326 MET cc_start: 0.8096 (tmm) cc_final: 0.7521 (tmm)
REVERT: A  409 MET cc_start: 0.6033 (mmp) cc_final: 0.5633 (tpp)
REVERT: A  468 PHE cc_start: 0.8234 (m-10) cc_final: 0.7880 (m-80)
REVERT: A  495 TYR cc_start: 0.7365 (OUTLIER) cc_final: 0.6485 (m-80)
REVERT: B  201 MET cc_start: 0.8725 (mpp) cc_final: 0.8405 (mpp)
REVERT: B  271 ASP cc_start: 0.8891 (t0) cc_final: 0.8664 (p0)
REVERT: B  310 MET cc_start: 0.8619 (ppp) cc_final: 0.8212 (ppp)
REVERT: B  326 MET cc_start: 0.6981 (tpt) cc_final: 0.6632 (tpt)
REVERT: B  338 GLU cc_start: 0.8643 (tp30) cc_final: 0.8292 (tp30)
REVERT: B  407 LEU cc_start: 0.9490 (tp) cc_final: 0.9034 (pp)
REVERT: B  413 LEU cc_start: 0.9120 (mm) cc_final: 0.8773 (pp)
REVERT: B  415 MET cc_start: 0.7912 (tpt) cc_final: 0.7559 (tpt)
REVERT: B  419 MET cc_start: 0.7905 (mmm) cc_final: 0.7467 (mmp)
REVERT: B  503 ILE cc_start: 0.8816 (mm) cc_final: 0.8558 (mp)
REVERT: B  550 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8488 (tm-30)
REVERT: B  657 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8352 (mp0)
REVERT: B  690 LEU cc_start: 0.9106 (tp) cc_final: 0.8821 (tp)
  outliers start: 35
  outliers final: 28
  residues processed: 163
  average time/residue: 0.0881
  time to fit residues: 20.6799
Evaluate side-chains
  168 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 134
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
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  217 ILE
Chi-restraints excluded: chain A residue  218 LEU
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  312 LEU
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  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  463 LEU
Chi-restraints excluded: chain A residue  495 TYR
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  250 PHE
Chi-restraints excluded: chain B residue  291 SER
Chi-restraints excluded: chain B residue  346 SER
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  458 LEU
Chi-restraints excluded: chain B residue  495 TYR
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  653 ASP
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:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0570
   chunk 18 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 104 optimal weight:    9.9990
   overall best weight:    1.1502

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 549 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.110375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.086033 restraints weight = 32267.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.088702 restraints weight = 18572.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.090453 restraints weight = 12926.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.091602 restraints weight = 10185.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.092200 restraints weight = 8720.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.5038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9050  Z= 0.132
  Angle     :  0.727  14.515  12278  Z= 0.348
  Chirality :  0.042   0.207   1498
  Planarity :  0.004   0.046   1522
  Dihedral  :  4.935  56.870   1218
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 23.33 %
    Favored  : 72.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.25), residues: 1122
  helix:  0.56 (0.20), residues: 710
  sheet:  0.30 (0.90), residues: 46
  loop : -2.28 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 627 
 TYR   0.026   0.001   TYR A 216 
 PHE   0.028   0.001   PHE B 308 
 TRP   0.003   0.000   TRP B 408 
 HIS   0.003   0.001   HIS A 490 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.13 ( 9050)
  covalent geometry    : angle       0.72701 /  0.35 (12278)
  hydrogen bonds       : bond        0.04887 /  3.25 (  481)
  hydrogen bonds       : angle       4.12078 /  2.85 ( 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
  175 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 135
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8770 (ppp) cc_final: 0.7366 (ppp)
REVERT: A  265 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6948 (pt)
REVERT: A  312 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8761 (pp)
REVERT: A  323 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7917 (t80)
REVERT: A  326 MET cc_start: 0.8193 (tmm) cc_final: 0.7660 (tmm)
REVERT: A  409 MET cc_start: 0.6088 (mmp) cc_final: 0.5677 (tpp)
REVERT: A  468 PHE cc_start: 0.8312 (m-10) cc_final: 0.7960 (m-80)
REVERT: A  495 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6556 (m-80)
REVERT: A  627 ARG cc_start: 0.7756 (mmp80) cc_final: 0.7383 (mmp80)
REVERT: B  201 MET cc_start: 0.8436 (mpp) cc_final: 0.8143 (mpp)
REVERT: B  254 MET cc_start: 0.8519 (tpp) cc_final: 0.8204 (tpp)
REVERT: B  326 MET cc_start: 0.7049 (tpt) cc_final: 0.6671 (tpt)
REVERT: B  338 GLU cc_start: 0.8669 (tp30) cc_final: 0.8316 (tp30)
REVERT: B  407 LEU cc_start: 0.9514 (tp) cc_final: 0.9058 (pp)
REVERT: B  503 ILE cc_start: 0.8793 (mm) cc_final: 0.8541 (mp)
REVERT: B  550 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8393 (tm-30)
REVERT: B  657 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8377 (mp0)
REVERT: B  678 LEU cc_start: 0.8882 (tp) cc_final: 0.8657 (tp)
REVERT: B  690 LEU cc_start: 0.9109 (tp) cc_final: 0.8842 (tp)
  outliers start: 40
  outliers final: 30
  residues processed: 159
  average time/residue: 0.0836
  time to fit residues: 19.2969
Evaluate side-chains
  170 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 134
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
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  217 ILE
Chi-restraints excluded: chain A residue  218 LEU
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  312 LEU
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  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  463 LEU
Chi-restraints excluded: chain A residue  495 TYR
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  250 PHE
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  346 SER
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  438 LEU
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  495 TYR
Chi-restraints excluded: chain B residue  549 ASN
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  653 ASP
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:    3.9990
   chunk 31 optimal weight:    0.0870
   chunk 99 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0050
   chunk 96 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.8174

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 445 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 = 0.3876 r_free = 0.3876 target = 0.110151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.085905 restraints weight = 31546.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.088738 restraints weight = 17583.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.090551 restraints weight = 11950.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.091730 restraints weight = 9266.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.092521 restraints weight = 7848.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.5170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9050  Z= 0.129
  Angle     :  0.741  14.009  12278  Z= 0.350
  Chirality :  0.042   0.197   1498
  Planarity :  0.004   0.046   1522
  Dihedral  :  4.915  57.208   1218
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 24.55 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.25), residues: 1122
  helix:  0.56 (0.20), residues: 710
  sheet:  0.33 (0.91), residues: 46
  loop : -2.30 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 593 
 TYR   0.024   0.001   TYR A 216 
 PHE   0.029   0.001   PHE B 308 
 TRP   0.018   0.002   TRP B 408 
 HIS   0.003   0.001   HIS A 490 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.13 ( 9050)
  covalent geometry    : angle       0.74105 /  0.35 (12278)
  hydrogen bonds       : bond        0.04851 /  3.24 (  481)
  hydrogen bonds       : angle       4.12380 /  2.85 ( 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
  175 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 142
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8813 (ppp) cc_final: 0.7305 (ppp)
REVERT: A  265 ILE cc_start: 0.7036 (OUTLIER) cc_final: 0.6690 (pt)
REVERT: A  312 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8759 (pp)
REVERT: A  323 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.8032 (t80)
REVERT: A  326 MET cc_start: 0.8139 (tmm) cc_final: 0.7605 (tmm)
REVERT: A  392 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8909 (tmtt)
REVERT: A  409 MET cc_start: 0.6050 (mmp) cc_final: 0.5665 (tpp)
REVERT: A  468 PHE cc_start: 0.8318 (m-10) cc_final: 0.7943 (m-80)
REVERT: A  495 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.6542 (m-80)
REVERT: B  201 MET cc_start: 0.8439 (mpp) cc_final: 0.8206 (mpp)
REVERT: B  254 MET cc_start: 0.8503 (tpp) cc_final: 0.8212 (tpp)
REVERT: B  326 MET cc_start: 0.7003 (tpt) cc_final: 0.6679 (tpt)
REVERT: B  338 GLU cc_start: 0.8647 (tp30) cc_final: 0.8311 (tp30)
REVERT: B  407 LEU cc_start: 0.9509 (tp) cc_final: 0.9076 (pp)
REVERT: B  415 MET cc_start: 0.8080 (tpt) cc_final: 0.7782 (tpt)
REVERT: B  503 ILE cc_start: 0.8826 (mm) cc_final: 0.8570 (mp)
REVERT: B  550 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8303 (tm-30)
REVERT: B  657 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8371 (mp0)
REVERT: B  678 LEU cc_start: 0.8839 (tp) cc_final: 0.8630 (tp)
REVERT: B  683 ARG cc_start: 0.8866 (mmm-85) cc_final: 0.8623 (mpt180)
REVERT: B  690 LEU cc_start: 0.9120 (tp) cc_final: 0.8846 (tp)
  outliers start: 33
  outliers final: 23
  residues processed: 160
  average time/residue: 0.0942
  time to fit residues: 21.2751
Evaluate side-chains
  163 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
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  217 ILE
Chi-restraints excluded: chain A residue  218 LEU
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  312 LEU
Chi-restraints excluded: chain A residue  323 PHE
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  463 LEU
Chi-restraints excluded: chain A residue  495 TYR
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  250 PHE
Chi-restraints excluded: chain B residue  346 SER
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  458 LEU
Chi-restraints excluded: chain B residue  495 TYR
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  653 ASP
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 6 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 109 optimal weight:   10.0000
   chunk 97 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 17 optimal weight:    0.1980
   chunk 111 optimal weight:   10.0000
   chunk 41 optimal weight:    0.0370
   chunk 75 optimal weight:    0.0970
   overall best weight:    0.4458

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 445 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 = 0.3901 r_free = 0.3901 target = 0.111809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.087597 restraints weight = 32104.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.090385 restraints weight = 18351.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.092180 restraints weight = 12659.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.093331 restraints weight = 9921.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.094039 restraints weight = 8481.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.5244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9050  Z= 0.127
  Angle     :  0.746  13.587  12278  Z= 0.351
  Chirality :  0.042   0.198   1498
  Planarity :  0.004   0.066   1522
  Dihedral  :  4.862  57.678   1218
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 25.05 %
    Favored  : 71.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.25), residues: 1122
  helix:  0.58 (0.20), residues: 714
  sheet:  0.38 (0.92), residues: 46
  loop : -2.26 (0.28), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 593 
 TYR   0.024   0.001   TYR A 216 
 PHE   0.030   0.001   PHE B 308 
 TRP   0.011   0.001   TRP B 408 
 HIS   0.003   0.001   HIS A 490 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.13 ( 9050)
  covalent geometry    : angle       0.74620 /  0.35 (12278)
  hydrogen bonds       : bond        0.04732 /  3.15 (  481)
  hydrogen bonds       : angle       4.05351 /  2.81 ( 1437)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1468.59 seconds
wall clock time: 26 minutes 1.01 seconds (1561.01 seconds total)