Starting phenix.real_space_refine
on Wed Apr 30 02:30:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k4b_36882/04_2025/8k4b_36882.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k4b_36882/04_2025/8k4b_36882.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k4b_36882/04_2025/8k4b_36882.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k4b_36882/04_2025/8k4b_36882.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k4b_36882/04_2025/8k4b_36882.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k4b_36882/04_2025/8k4b_36882.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.029
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.10, per 1000 atoms: 0.68
  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: 2.80
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 1.21
  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: 2.43

  Time building geometry restraints manager: 3.04 seconds

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

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

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

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

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

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

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

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.05
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:                  0.010
  Normalize map: mean=0, sd=1:             0.600
  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:             0.020
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.110
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.040
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.101   9050  Z= 0.482
  Angle     :  1.397  16.379  12278  Z= 0.795
  Chirality :  0.067   0.375   1498
  Planarity :  0.008   0.098   1522
  Dihedral  : 15.605  88.080   3394
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 8.38
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.017   0.004   TRP A 408 
 HIS   0.003   0.001   HIS A 490 
 PHE   0.022   0.002   PHE A 434 
 TYR   0.034   0.002   TYR B 188 
 ARG   0.007   0.001   ARG B 627 

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

*********************** 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  : 1.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8531 (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: 0.7999 (mmt)
REVERT: A  312 LEU cc_start: 0.9177 (tp) cc_final: 0.8742 (pp)
REVERT: A  409 MET cc_start: 0.6014 (mmp) cc_final: 0.5775 (tmm)
REVERT: A  492 LYS cc_start: 0.8580 (tppt) cc_final: 0.8139 (mmtt)
REVERT: A  609 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6848 (pp)
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: 0.7896 (tp)
  outliers start: 9
  outliers final: 2
  residues processed: 261
  average time/residue: 0.2431
  time to fit residues: 83.4739
Evaluate side-chains
  162 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 158
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain A residue  247 LYS
Chi-restraints excluded: chain A residue  609 LEU
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 94 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 65 optimal weight:    0.4980
   chunk 101 optimal weight:    4.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 352 ASN
A 455 ASN
** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 352 ASN
B 455 ASN
B 550 GLN
** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.111601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.086859 restraints weight = 29615.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.089578 restraints weight = 16835.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.091404 restraints weight = 11496.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9050  Z= 0.146
  Angle     :  0.745  13.116  12278  Z= 0.373
  Chirality :  0.041   0.177   1498
  Planarity :  0.005   0.075   1522
  Dihedral  :  8.731  79.064   1292
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 12.02 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.24), residues: 1122
  helix: -0.57 (0.19), residues: 712
  sheet:  0.32 (0.95), residues: 46
  loop : -2.72 (0.26), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 408 
 HIS   0.003   0.001   HIS A 490 
 PHE   0.020   0.002   PHE B 434 
 TYR   0.024   0.002   TYR A 216 
 ARG   0.005   0.001   ARG B 260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05784 (  481)
  hydrogen bonds       : angle       4.70500 ( 1437)
  covalent geometry    : bond        0.00300 ( 9050)
  covalent geometry    : angle       0.74468 (12278)

*********************** 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
  209 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 173
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8829 (ppp) cc_final: 0.8615 (ppp)
REVERT: A  323 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7651 (t80)
REVERT: A  326 MET cc_start: 0.7859 (tmm) cc_final: 0.7136 (tmm)
REVERT: A  409 MET cc_start: 0.6436 (mmp) cc_final: 0.6147 (tpp)
REVERT: A  468 PHE cc_start: 0.8328 (m-10) cc_final: 0.8068 (m-80)
REVERT: A  626 GLN cc_start: 0.8710 (mp10) cc_final: 0.8350 (mp10)
REVERT: A  627 ARG cc_start: 0.7968 (mmp80) cc_final: 0.7603 (mmp80)
REVERT: B  231 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.6026 (mp)
REVERT: B  326 MET cc_start: 0.6961 (tpt) cc_final: 0.6652 (tpt)
REVERT: B  503 ILE cc_start: 0.8924 (mm) cc_final: 0.8637 (mp)
REVERT: B  550 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8357 (tm-30)
REVERT: B  657 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8427 (mp0)
REVERT: B  690 LEU cc_start: 0.8962 (tp) cc_final: 0.8553 (tp)
REVERT: B  711 TYR cc_start: 0.8591 (t80) cc_final: 0.8222 (t80)
  outliers start: 36
  outliers final: 19
  residues processed: 192
  average time/residue: 0.2013
  time to fit residues: 53.5771
Evaluate side-chains
  170 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
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  371 ASP
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  231 LEU
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  241 VAL
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  424 LEU
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  497 ARG
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  559 TYR
Chi-restraints excluded: chain B residue  644 ILE
Chi-restraints excluded: chain B residue  657 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 87 optimal weight:    0.4980
   chunk 71 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 102 optimal weight:    5.9990
   chunk 46 optimal weight:    9.9990
   chunk 78 optimal weight:    2.9990
   chunk 95 optimal weight:    9.9990
   chunk 3 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    2.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 HIS
A 352 ASN
A 456 ASN
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 455 ASN
B 550 GLN
B 566 GLN
** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 612 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.105632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.080884 restraints weight = 30871.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.083481 restraints weight = 17544.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.085195 restraints weight = 12020.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.4100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9050  Z= 0.192
  Angle     :  0.753  11.262  12278  Z= 0.382
  Chirality :  0.042   0.188   1498
  Planarity :  0.005   0.065   1522
  Dihedral  :  8.180  84.779   1283
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 15.35 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.24), residues: 1122
  helix: -0.06 (0.19), residues: 712
  sheet:  0.31 (0.92), residues: 46
  loop : -2.39 (0.28), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 408 
 HIS   0.004   0.001   HIS A 490 
 PHE   0.028   0.002   PHE B 308 
 TYR   0.017   0.002   TYR A 216 
 ARG   0.004   0.001   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06043 (  481)
  hydrogen bonds       : angle       4.64670 ( 1437)
  covalent geometry    : bond        0.00424 ( 9050)
  covalent geometry    : angle       0.75316 (12278)

*********************** 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
  203 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 159
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8896 (ppp) cc_final: 0.7850 (ppp)
REVERT: A  326 MET cc_start: 0.8221 (tmm) cc_final: 0.7615 (tmm)
REVERT: A  607 MET cc_start: 0.7212 (mpp) cc_final: 0.6910 (mpp)
REVERT: B  196 TYR cc_start: 0.5209 (t80) cc_final: 0.4110 (t80)
REVERT: B  260 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.7061 (mmm-85)
REVERT: B  455 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8817 (t0)
REVERT: B  503 ILE cc_start: 0.8908 (mm) cc_final: 0.8624 (mp)
REVERT: B  550 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8678 (tm-30)
REVERT: B  690 LEU cc_start: 0.9046 (tp) cc_final: 0.8710 (tp)
REVERT: B  701 HIS cc_start: 0.9225 (OUTLIER) cc_final: 0.8584 (t70)
REVERT: B  711 TYR cc_start: 0.8691 (t80) cc_final: 0.8213 (t80)
  outliers start: 44
  outliers final: 31
  residues processed: 188
  average time/residue: 0.1853
  time to fit residues: 49.4380
Evaluate side-chains
  175 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 141
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  371 ASP
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 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  283 ILE
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  425 ILE
Chi-restraints excluded: chain B residue  432 VAL
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  497 ARG
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
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 48 optimal weight:    0.6980
   chunk 14 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9990
   chunk 89 optimal weight:    5.9990
   chunk 66 optimal weight:    4.9990
   chunk 99 optimal weight:    8.9990
   chunk 40 optimal weight:    0.7980
   chunk 109 optimal weight:    1.9990
   chunk 108 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 251 HIS
A 456 ASN
B 219 GLN
B 550 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.106571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.081937 restraints weight = 31032.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.084612 restraints weight = 17553.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.086326 restraints weight = 11999.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.4410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9050  Z= 0.142
  Angle     :  0.706  11.407  12278  Z= 0.345
  Chirality :  0.041   0.189   1498
  Planarity :  0.004   0.059   1522
  Dihedral  :  7.660  81.407   1283
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 20.61 %
    Favored  : 75.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.25), residues: 1122
  helix:  0.22 (0.20), residues: 712
  sheet:  0.50 (0.93), residues: 46
  loop : -2.29 (0.28), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 408 
 HIS   0.004   0.001   HIS A 490 
 PHE   0.027   0.001   PHE B 308 
 TYR   0.031   0.001   TYR A 216 
 ARG   0.004   0.000   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05485 (  481)
  hydrogen bonds       : angle       4.33333 ( 1437)
  covalent geometry    : bond        0.00308 ( 9050)
  covalent geometry    : angle       0.70558 (12278)

*********************** 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
  192 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 153
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8967 (ppp) cc_final: 0.7817 (ppp)
REVERT: A  312 LEU cc_start: 0.9222 (tt) cc_final: 0.8733 (pp)
REVERT: A  323 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7744 (t80)
REVERT: A  326 MET cc_start: 0.8235 (tmm) cc_final: 0.7737 (tmm)
REVERT: A  607 MET cc_start: 0.7072 (mpp) cc_final: 0.6717 (mpp)
REVERT: A  622 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8492 (pt)
REVERT: B  196 TYR cc_start: 0.5016 (t80) cc_final: 0.4057 (t80)
REVERT: B  260 ARG cc_start: 0.7345 (ttm-80) cc_final: 0.6985 (mmm-85)
REVERT: B  326 MET cc_start: 0.6868 (tpt) cc_final: 0.6494 (tpt)
REVERT: B  407 LEU cc_start: 0.9520 (tp) cc_final: 0.9044 (pp)
REVERT: B  419 MET cc_start: 0.8092 (mmp) cc_final: 0.7776 (mmp)
REVERT: B  497 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7349 (ptp-170)
REVERT: B  503 ILE cc_start: 0.8942 (mm) cc_final: 0.8674 (mp)
REVERT: B  550 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8516 (tm-30)
REVERT: B  657 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8352 (mp0)
REVERT: B  690 LEU cc_start: 0.9040 (tp) cc_final: 0.8754 (tp)
REVERT: B  711 TYR cc_start: 0.8757 (t80) cc_final: 0.8486 (t80)
  outliers start: 39
  outliers final: 23
  residues processed: 173
  average time/residue: 0.1967
  time to fit residues: 48.3854
Evaluate side-chains
  167 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 139
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  371 ASP
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  217 ILE
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  250 PHE
Chi-restraints excluded: chain B residue  319 THR
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  448 LEU
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  495 TYR
Chi-restraints excluded: chain B residue  497 ARG
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 36 optimal weight:    0.5980
   chunk 105 optimal weight:   10.0000
   chunk 104 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   chunk 6 optimal weight:    0.2980
   chunk 72 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 59 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    0.7582

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.107786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.083227 restraints weight = 30913.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.085938 restraints weight = 17486.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.087729 restraints weight = 11961.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.4584

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= 0.126
  Angle     :  0.709  11.811  12278  Z= 0.340
  Chirality :  0.041   0.301   1498
  Planarity :  0.004   0.054   1522
  Dihedral  :  7.275  81.191   1280
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 21.82 %
    Favored  : 74.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.25), residues: 1122
  helix:  0.35 (0.20), residues: 714
  sheet:  0.40 (0.91), residues: 46
  loop : -2.37 (0.27), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 408 
 HIS   0.003   0.001   HIS A 490 
 PHE   0.028   0.001   PHE B 308 
 TYR   0.031   0.001   TYR A 216 
 ARG   0.004   0.000   ARG B 386 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05129 (  481)
  hydrogen bonds       : angle       4.18933 ( 1437)
  covalent geometry    : bond        0.00261 ( 9050)
  covalent geometry    : angle       0.70933 (12278)

*********************** 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
  190 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 151
  time to evaluate  : 1.117 
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: 0.8946 (ppp) cc_final: 0.7714 (ppp)
REVERT: A  265 ILE cc_start: 0.7222 (OUTLIER) cc_final: 0.6957 (pt)
REVERT: A  312 LEU cc_start: 0.9228 (tt) cc_final: 0.8768 (pp)
REVERT: A  323 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7775 (t80)
REVERT: A  326 MET cc_start: 0.8233 (tmm) cc_final: 0.7803 (tmm)
REVERT: A  607 MET cc_start: 0.6836 (mpp) cc_final: 0.6462 (mpp)
REVERT: B  196 TYR cc_start: 0.4779 (t80) cc_final: 0.3834 (t80)
REVERT: B  260 ARG cc_start: 0.7358 (ttm-80) cc_final: 0.7020 (mmm-85)
REVERT: B  271 ASP cc_start: 0.9006 (t70) cc_final: 0.8762 (p0)
REVERT: B  326 MET cc_start: 0.6875 (tpt) cc_final: 0.6522 (tpt)
REVERT: B  338 GLU cc_start: 0.8758 (tp30) cc_final: 0.8454 (tp30)
REVERT: B  407 LEU cc_start: 0.9544 (tp) cc_final: 0.9075 (pp)
REVERT: B  419 MET cc_start: 0.7966 (mmp) cc_final: 0.7732 (mmm)
REVERT: B  497 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7302 (ptp-170)
REVERT: B  503 ILE cc_start: 0.8908 (mm) cc_final: 0.8634 (mp)
REVERT: B  550 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8486 (tm-30)
REVERT: B  678 LEU cc_start: 0.8741 (tp) cc_final: 0.8532 (tp)
REVERT: B  690 LEU cc_start: 0.9052 (tp) cc_final: 0.8777 (tp)
REVERT: B  701 HIS cc_start: 0.9262 (OUTLIER) cc_final: 0.8681 (t-90)
REVERT: B  711 TYR cc_start: 0.8739 (t80) cc_final: 0.8458 (t80)
  outliers start: 39
  outliers final: 21
  residues processed: 175
  average time/residue: 0.2130
  time to fit residues: 53.0064
Evaluate side-chains
  167 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  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  497 ARG
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  653 ASP
Chi-restraints excluded: chain B residue  657 GLU
Chi-restraints excluded: chain B residue  684 THR
Chi-restraints excluded: chain B residue  701 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 32 optimal weight:    0.4980
   chunk 40 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 16 optimal weight:    0.3980
   chunk 77 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.7182

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.108447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.083980 restraints weight = 30959.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.086697 restraints weight = 17518.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.088470 restraints weight = 12001.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.4782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9050  Z= 0.127
  Angle     :  0.708  12.247  12278  Z= 0.341
  Chirality :  0.041   0.252   1498
  Planarity :  0.004   0.051   1522
  Dihedral  :  7.100  86.374   1280
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 23.03 %
    Favored  : 73.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.25), residues: 1122
  helix:  0.38 (0.20), residues: 716
  sheet:  0.47 (0.92), residues: 46
  loop : -2.32 (0.27), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 408 
 HIS   0.003   0.001   HIS A 490 
 PHE   0.029   0.001   PHE B 308 
 TYR   0.032   0.001   TYR A 216 
 ARG   0.005   0.000   ARG A 627 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04935 (  481)
  hydrogen bonds       : angle       4.14381 ( 1437)
  covalent geometry    : bond        0.00258 ( 9050)
  covalent geometry    : angle       0.70822 (12278)

*********************** 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
  188 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 154
  time to evaluate  : 1.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8884 (ppp) cc_final: 0.7571 (ppp)
REVERT: A  265 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6843 (pt)
REVERT: A  312 LEU cc_start: 0.9198 (tt) cc_final: 0.8744 (pp)
REVERT: A  323 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7898 (t80)
REVERT: A  326 MET cc_start: 0.8199 (tmm) cc_final: 0.7777 (tmm)
REVERT: A  392 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8870 (tmtt)
REVERT: A  409 MET cc_start: 0.6607 (mmp) cc_final: 0.6182 (tpp)
REVERT: A  568 TYR cc_start: 0.9081 (t80) cc_final: 0.8764 (t80)
REVERT: A  607 MET cc_start: 0.6717 (mpp) cc_final: 0.6363 (mpp)
REVERT: B  196 TYR cc_start: 0.4910 (t80) cc_final: 0.3972 (t80)
REVERT: B  260 ARG cc_start: 0.7237 (ttm-80) cc_final: 0.6897 (mmm-85)
REVERT: B  271 ASP cc_start: 0.8980 (t70) cc_final: 0.8775 (p0)
REVERT: B  326 MET cc_start: 0.6822 (tpt) cc_final: 0.6547 (tpt)
REVERT: B  338 GLU cc_start: 0.8730 (tp30) cc_final: 0.8416 (tp30)
REVERT: B  419 MET cc_start: 0.7960 (mmp) cc_final: 0.7725 (mmm)
REVERT: B  497 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7240 (ptp-170)
REVERT: B  503 ILE cc_start: 0.8897 (mm) cc_final: 0.8635 (mp)
REVERT: B  550 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8518 (tm-30)
REVERT: B  657 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8372 (mp0)
REVERT: B  690 LEU cc_start: 0.9087 (tp) cc_final: 0.8806 (tp)
REVERT: B  701 HIS cc_start: 0.9268 (OUTLIER) cc_final: 0.8842 (t-90)
  outliers start: 34
  outliers final: 22
  residues processed: 176
  average time/residue: 0.2254
  time to fit residues: 57.4520
Evaluate side-chains
  166 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 137
  time to evaluate  : 1.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  392 LYS
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  441 ILE
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  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  497 ARG
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  653 ASP
Chi-restraints excluded: chain B residue  657 GLU
Chi-restraints excluded: chain B residue  684 THR
Chi-restraints excluded: chain B residue  701 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 110 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 107 optimal weight:    6.9990
   chunk 66 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   chunk 96 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 56 optimal weight:    9.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 550 GLN
B 676 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.105961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.081492 restraints weight = 31512.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.084124 restraints weight = 17906.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.085842 restraints weight = 12282.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.5082

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= 0.153
  Angle     :  0.732  12.882  12278  Z= 0.355
  Chirality :  0.042   0.206   1498
  Planarity :  0.004   0.050   1522
  Dihedral  :  7.065  88.430   1280
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 23.33 %
    Favored  : 72.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.25), residues: 1122
  helix:  0.33 (0.20), residues: 722
  sheet:  0.39 (0.92), residues: 46
  loop : -2.40 (0.28), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 408 
 HIS   0.004   0.001   HIS B 713 
 PHE   0.029   0.001   PHE B 308 
 TYR   0.032   0.001   TYR A 216 
 ARG   0.005   0.001   ARG A 593 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05312 (  481)
  hydrogen bonds       : angle       4.27521 ( 1437)
  covalent geometry    : bond        0.00338 ( 9050)
  covalent geometry    : angle       0.73222 (12278)

*********************** 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
  176 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 138
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8908 (ppp) cc_final: 0.7537 (ppp)
REVERT: A  312 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8735 (pp)
REVERT: A  326 MET cc_start: 0.8165 (tmm) cc_final: 0.7833 (tpp)
REVERT: A  392 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8806 (tmtt)
REVERT: A  495 TYR cc_start: 0.7535 (OUTLIER) cc_final: 0.6567 (m-80)
REVERT: A  607 MET cc_start: 0.7035 (mpp) cc_final: 0.6348 (mpp)
REVERT: B  260 ARG cc_start: 0.7356 (ttm-80) cc_final: 0.7051 (mmm-85)
REVERT: B  271 ASP cc_start: 0.9017 (t70) cc_final: 0.8787 (p0)
REVERT: B  326 MET cc_start: 0.7103 (tpt) cc_final: 0.6641 (tpt)
REVERT: B  407 LEU cc_start: 0.9548 (tp) cc_final: 0.9090 (pp)
REVERT: B  497 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7063 (ptp-170)
REVERT: B  503 ILE cc_start: 0.8926 (mm) cc_final: 0.8669 (mp)
REVERT: B  550 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8532 (tm-30)
REVERT: B  657 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8385 (mp0)
REVERT: B  690 LEU cc_start: 0.9114 (tp) cc_final: 0.8870 (tp)
  outliers start: 38
  outliers final: 27
  residues processed: 160
  average time/residue: 0.1939
  time to fit residues: 44.5259
Evaluate side-chains
  169 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 136
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  239 ILE
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  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  497 ARG
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  657 GLU
Chi-restraints excluded: chain B residue  684 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 104 optimal weight:    0.0570
   chunk 14 optimal weight:    2.9990
   chunk 98 optimal weight:    6.9990
   chunk 85 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 38 optimal weight:   30.0000
   chunk 105 optimal weight:    5.9990
   chunk 84 optimal weight:    0.0170
   chunk 62 optimal weight:    7.9990
   chunk 101 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    0.7740

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 549 ASN
B 550 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.107915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.083472 restraints weight = 31341.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.086197 restraints weight = 17649.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.087951 restraints weight = 12012.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.5178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9050  Z= 0.126
  Angle     :  0.719  13.400  12278  Z= 0.343
  Chirality :  0.041   0.202   1498
  Planarity :  0.004   0.049   1522
  Dihedral  :  6.840  87.095   1280
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 23.94 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.25), residues: 1122
  helix:  0.45 (0.20), residues: 714
  sheet:  0.36 (0.92), residues: 46
  loop : -2.30 (0.27), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B 408 
 HIS   0.003   0.001   HIS B 701 
 PHE   0.028   0.001   PHE B 308 
 TYR   0.032   0.001   TYR A 216 
 ARG   0.008   0.001   ARG A 593 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04964 (  481)
  hydrogen bonds       : angle       4.14674 ( 1437)
  covalent geometry    : bond        0.00260 ( 9050)
  covalent geometry    : angle       0.71906 (12278)

*********************** 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
  175 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 141
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8868 (ppp) cc_final: 0.7475 (ppp)
REVERT: A  312 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8714 (pp)
REVERT: A  323 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.8004 (t80)
REVERT: A  326 MET cc_start: 0.8250 (tmm) cc_final: 0.7938 (tpp)
REVERT: A  392 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8781 (tmtt)
REVERT: A  409 MET cc_start: 0.6357 (mmp) cc_final: 0.5975 (tpp)
REVERT: A  419 MET cc_start: 0.8324 (mmp) cc_final: 0.7529 (ttt)
REVERT: A  495 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.6523 (m-80)
REVERT: A  568 TYR cc_start: 0.9108 (t80) cc_final: 0.8769 (t80)
REVERT: A  607 MET cc_start: 0.6924 (mpp) cc_final: 0.6221 (mpp)
REVERT: B  196 TYR cc_start: 0.4800 (t80) cc_final: 0.4402 (t80)
REVERT: B  201 MET cc_start: 0.9218 (mpp) cc_final: 0.8577 (mpp)
REVERT: B  260 ARG cc_start: 0.7138 (ttm-80) cc_final: 0.6829 (mmm-85)
REVERT: B  326 MET cc_start: 0.7051 (tpt) cc_final: 0.6777 (tpt)
REVERT: B  407 LEU cc_start: 0.9550 (tp) cc_final: 0.9098 (pp)
REVERT: B  419 MET cc_start: 0.7724 (mmp) cc_final: 0.7488 (mmp)
REVERT: B  497 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6998 (ptp-170)
REVERT: B  503 ILE cc_start: 0.8895 (mm) cc_final: 0.8641 (mp)
REVERT: B  550 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8471 (tm-30)
REVERT: B  657 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8281 (mp0)
REVERT: B  690 LEU cc_start: 0.9107 (tp) cc_final: 0.8851 (tp)
  outliers start: 34
  outliers final: 23
  residues processed: 161
  average time/residue: 0.2325
  time to fit residues: 53.5580
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  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  284 LEU
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  392 LYS
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  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  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  495 TYR
Chi-restraints excluded: chain B residue  497 ARG
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  657 GLU
Chi-restraints excluded: chain B residue  684 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   chunk 34 optimal weight:    9.9990
   chunk 35 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0020
   chunk 71 optimal weight:    8.9990
   chunk 8 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.1394

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.107141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.082849 restraints weight = 31164.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.085536 restraints weight = 17615.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.087307 restraints weight = 12037.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.5307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9050  Z= 0.134
  Angle     :  0.748  13.722  12278  Z= 0.351
  Chirality :  0.043   0.323   1498
  Planarity :  0.004   0.048   1522
  Dihedral  :  6.752  87.253   1280
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 24.44 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.25), residues: 1122
  helix:  0.45 (0.20), residues: 708
  sheet:  0.41 (0.93), residues: 46
  loop : -2.24 (0.28), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 408 
 HIS   0.003   0.001   HIS A 490 
 PHE   0.021   0.001   PHE B 434 
 TYR   0.031   0.001   TYR A 216 
 ARG   0.008   0.001   ARG A 593 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05025 (  481)
  hydrogen bonds       : angle       4.25291 ( 1437)
  covalent geometry    : bond        0.00290 ( 9050)
  covalent geometry    : angle       0.74823 (12278)

*********************** 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
  172 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 138
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.7483 (ppp)
REVERT: A  312 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8722 (pp)
REVERT: A  326 MET cc_start: 0.8241 (tmm) cc_final: 0.7933 (tpp)
REVERT: A  392 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8763 (tmtt)
REVERT: A  409 MET cc_start: 0.6320 (mmp) cc_final: 0.5929 (tpp)
REVERT: A  419 MET cc_start: 0.8316 (mmp) cc_final: 0.7380 (ttt)
REVERT: A  433 TYR cc_start: 0.6192 (m-80) cc_final: 0.5942 (m-10)
REVERT: A  495 TYR cc_start: 0.7458 (OUTLIER) cc_final: 0.6575 (m-80)
REVERT: A  568 TYR cc_start: 0.9109 (t80) cc_final: 0.8762 (t80)
REVERT: A  607 MET cc_start: 0.6918 (mpp) cc_final: 0.6226 (mpp)
REVERT: A  664 LEU cc_start: 0.9533 (tp) cc_final: 0.9168 (pp)
REVERT: B  196 TYR cc_start: 0.4931 (t80) cc_final: 0.4512 (t80)
REVERT: B  260 ARG cc_start: 0.7142 (ttm-80) cc_final: 0.6834 (mmm-85)
REVERT: B  326 MET cc_start: 0.7076 (tpt) cc_final: 0.6763 (tpt)
REVERT: B  407 LEU cc_start: 0.9551 (tp) cc_final: 0.9101 (pp)
REVERT: B  497 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6973 (ptp-170)
REVERT: B  503 ILE cc_start: 0.8886 (mm) cc_final: 0.8633 (mp)
REVERT: B  550 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8489 (tm-30)
REVERT: B  657 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8308 (mp0)
REVERT: B  690 LEU cc_start: 0.9112 (tp) cc_final: 0.8871 (tp)
  outliers start: 34
  outliers final: 25
  residues processed: 155
  average time/residue: 0.2329
  time to fit residues: 52.3208
Evaluate side-chains
  163 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  201 MET
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  250 PHE
Chi-restraints excluded: chain B residue  335 ASP
Chi-restraints excluded: chain B residue  346 SER
Chi-restraints excluded: chain B residue  373 GLU
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  497 ARG
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  657 GLU
Chi-restraints excluded: chain B residue  684 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   chunk 18 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 111 optimal weight:    1.9990
   overall best weight:    1.1786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.108448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.083895 restraints weight = 32537.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.086659 restraints weight = 18339.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.088452 restraints weight = 12521.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.5468

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= 0.136
  Angle     :  0.754  14.166  12278  Z= 0.357
  Chirality :  0.043   0.272   1498
  Planarity :  0.004   0.076   1522
  Dihedral  :  6.691  86.549   1280
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 25.45 %
    Favored  : 71.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.25), residues: 1122
  helix:  0.41 (0.20), residues: 708
  sheet:  0.38 (0.92), residues: 46
  loop : -2.24 (0.28), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 408 
 HIS   0.003   0.001   HIS A 490 
 PHE   0.022   0.001   PHE B 434 
 TYR   0.030   0.001   TYR A 216 
 ARG   0.015   0.001   ARG A 593 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05064 (  481)
  hydrogen bonds       : angle       4.27026 ( 1437)
  covalent geometry    : bond        0.00295 ( 9050)
  covalent geometry    : angle       0.75359 (12278)

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

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 132
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.7451 (ppp)
REVERT: A  312 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8708 (pp)
REVERT: A  326 MET cc_start: 0.8200 (tmm) cc_final: 0.7909 (tpp)
REVERT: A  392 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8789 (tmtt)
REVERT: A  409 MET cc_start: 0.6322 (mmp) cc_final: 0.5936 (tpp)
REVERT: A  419 MET cc_start: 0.8463 (mmp) cc_final: 0.7367 (ttt)
REVERT: A  495 TYR cc_start: 0.7497 (OUTLIER) cc_final: 0.6521 (m-80)
REVERT: A  568 TYR cc_start: 0.9171 (t80) cc_final: 0.8903 (t80)
REVERT: A  606 ARG cc_start: 0.8106 (ptp90) cc_final: 0.6086 (ptt-90)
REVERT: A  607 MET cc_start: 0.6861 (mpp) cc_final: 0.6284 (mpp)
REVERT: A  664 LEU cc_start: 0.9591 (tp) cc_final: 0.9203 (pp)
REVERT: B  196 TYR cc_start: 0.5134 (t80) cc_final: 0.4725 (t80)
REVERT: B  260 ARG cc_start: 0.7130 (ttm-80) cc_final: 0.6835 (mmm-85)
REVERT: B  326 MET cc_start: 0.7011 (tpt) cc_final: 0.6698 (tpt)
REVERT: B  407 LEU cc_start: 0.9585 (tp) cc_final: 0.9138 (pp)
REVERT: B  497 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7061 (ptp-170)
REVERT: B  503 ILE cc_start: 0.8965 (mm) cc_final: 0.8710 (mp)
REVERT: B  550 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8426 (tm-30)
REVERT: B  657 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8392 (mp0)
REVERT: B  690 LEU cc_start: 0.9135 (tp) cc_final: 0.8896 (tp)
  outliers start: 33
  outliers final: 23
  residues processed: 150
  average time/residue: 0.2706
  time to fit residues: 59.7625
Evaluate side-chains
  160 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  201 MET
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  317 ILE
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  432 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  250 PHE
Chi-restraints excluded: chain B residue  335 ASP
Chi-restraints excluded: chain B residue  346 SER
Chi-restraints excluded: chain B residue  373 GLU
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  497 ARG
Chi-restraints excluded: chain B residue  550 GLN
Chi-restraints excluded: chain B residue  657 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   chunk 64 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 81 optimal weight:    9.9990
   chunk 16 optimal weight:    0.0770
   chunk 23 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 91 optimal weight:   10.0000
   overall best weight:    1.3944

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.107931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.083405 restraints weight = 32810.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.086131 restraints weight = 18343.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.087912 restraints weight = 12527.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.5577

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= 0.142
  Angle     :  0.766  14.376  12278  Z= 0.361
  Chirality :  0.043   0.261   1498
  Planarity :  0.004   0.048   1522
  Dihedral  :  6.648  85.457   1280
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 25.66 %
    Favored  : 71.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.25), residues: 1122
  helix:  0.45 (0.20), residues: 702
  sheet:  0.26 (0.90), residues: 46
  loop : -2.17 (0.28), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 408 
 HIS   0.003   0.001   HIS A 490 
 PHE   0.024   0.001   PHE B 434 
 TYR   0.028   0.001   TYR A 216 
 ARG   0.006   0.001   ARG A 627 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05118 (  481)
  hydrogen bonds       : angle       4.29227 ( 1437)
  covalent geometry    : bond        0.00314 ( 9050)
  covalent geometry    : angle       0.76580 (12278)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3368.97 seconds
wall clock time: 61 minutes 38.03 seconds (3698.03 seconds total)