Starting phenix.real_space_refine
on Sat Aug 23 02:06:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k7a_36936/08_2025/8k7a_36936.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k7a_36936/08_2025/8k7a_36936.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k7a_36936/08_2025/8k7a_36936.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k7a_36936/08_2025/8k7a_36936.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k7a_36936/08_2025/8k7a_36936.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k7a_36936/08_2025/8k7a_36936.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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
     P       6      5.49       5
     Mg      2      5.21       5
     S      28      5.16       5
     C    5732      2.51       5
     N    1464      2.21       5
     O    1686      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8918
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 563, 4427
          Classifications: {'peptide': 563}
          Link IDs: {'PTRANS': 12, 'TRANS': 550}
    Chain: "B"
      Number of atoms: 4427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 563, 4427
          Classifications: {'peptide': 563}
          Link IDs: {'PTRANS': 12, 'TRANS': 550}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 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: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.54, per 1000 atoms: 0.28
  Number of scatterers: 8918
  At special positions: 0
  Unit cell: (82.368, 80.652, 141.57, 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)
     S      28     16.00
     P       6     15.00
     Mg      2     11.99
     O    1686      8.00
     N    1464      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.07
  Conformation dependent library (CDL) restraints added in 399.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 4 sheets defined
      67.1% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 158 through 162
    Processing helix  chain 'A' and resid 168 through 173
      removed outlier: 4.322A  pdb=" N   VAL A 172 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 188
      removed outlier: 3.686A  pdb=" N   THR A 179 " --> pdb=" O   THR A 175 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ASN A 182 " --> pdb=" O   VAL A 178 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   SER A 186 " --> pdb=" O   ASN A 182 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   TYR A 188 " --> pdb=" O   VAL A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 251
      removed outlier: 4.430A  pdb=" N   LEU A 218 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLN A 219 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   GLN A 220 " --> pdb=" O   TYR A 216 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   VAL A 232 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   ASP A 240 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   VAL A 241 " --> pdb=" O   LEU A 237 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   TYR A 245 " --> pdb=" O   VAL A 241 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE A 246 " --> pdb=" O   ILE A 242 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   HIS A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 260
      removed outlier: 4.371A  pdb=" N   PHE A 257 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 272
      removed outlier: 3.945A  pdb=" N   ARG A 268 " --> pdb=" O   GLU A 264 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   PHE A 269 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 292
      removed outlier: 4.528A  pdb=" N   ILE A 276 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   ASP A 277 " --> pdb=" O   ASN A 273 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ALA A 278 " --> pdb=" O   SER A 274 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ALA A 280 " --> pdb=" O   ILE A 276 " (cutoff:3.500A)
      removed outlier: 5.412A  pdb=" N   VAL A 290 " --> pdb=" O   ILE A 286 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   THR A 292 " --> pdb=" O   LEU A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 304
      removed outlier: 3.973A  pdb=" N   LEU A 298 " --> pdb=" O   VAL A 294 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   VAL A 299 " --> pdb=" O   ILE A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 312
    Processing helix  chain 'A' and resid 313 through 325
      removed outlier: 4.309A  pdb=" N   ILE A 317 " --> pdb=" O   LEU A 313 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   PHE A 325 " --> pdb=" O   ILE A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 352
      removed outlier: 4.540A  pdb=" N   GLU A 330 " --> pdb=" O   MET A 326 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   LYS A 331 " --> pdb=" O   LYS A 327 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   MET A 332 " --> pdb=" O   PRO A 328 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ASP A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   MET A 337 " --> pdb=" O   ASN A 333 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   GLU A 338 " --> pdb=" O   ARG A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 361
      removed outlier: 4.162A  pdb=" N   ILE A 357 " --> pdb=" O   GLY A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 416
      removed outlier: 3.919A  pdb=" N   ARG A 366 " --> pdb=" O   SER A 362 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LYS A 369 " --> pdb=" O   GLN A 365 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   VAL A 412 " --> pdb=" O   TRP A 408 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   LEU A 413 " --> pdb=" O   MET A 409 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL A 414 " --> pdb=" O   GLY A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 444
      removed outlier: 3.964A  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 461
      removed outlier: 3.767A  pdb=" N   THR A 450 " --> pdb=" O   THR A 446 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   VAL A 461 " --> pdb=" O   ARG A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 531
      removed outlier: 3.627A  pdb=" N   ALA A 527 " --> pdb=" O   LYS A 523 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL A 531 " --> pdb=" O   ALA A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 559
      removed outlier: 3.759A  pdb=" N   LEU A 556 " --> pdb=" O   ASP A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 579
    Processing helix  chain 'A' and resid 588 through 598
    Processing helix  chain 'A' and resid 623 through 638
      removed outlier: 3.879A  pdb=" N   THR A 638 " --> pdb=" O   ARG A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 665
      removed outlier: 3.502A  pdb=" N   ILE A 665 " --> pdb=" O   VAL A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 683
      removed outlier: 4.339A  pdb=" N   ALA A 681 " --> pdb=" O   ARG A 677 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLU A 682 " --> pdb=" O   LEU A 678 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   ARG A 683 " --> pdb=" O   THR A 679 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 677 through 683'
    Processing helix  chain 'A' and resid 700 through 707
    Processing helix  chain 'A' and resid 709 through 717
      removed outlier: 3.524A  pdb=" N   HIS A 713 " --> pdb=" O   GLY A 709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 164
      removed outlier: 3.910A  pdb=" N   LYS B 163 " --> pdb=" O   PRO B 159 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLN B 164 " --> pdb=" O   ILE B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 190
      removed outlier: 3.983A  pdb=" N   ILE B 171 " --> pdb=" O   LEU B 167 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL B 172 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LEU B 173 " --> pdb=" O   ALA B 169 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA B 174 " --> pdb=" O   ASN B 170 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU B 177 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   VAL B 178 " --> pdb=" O   ALA B 174 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   THR B 179 " --> pdb=" O   THR B 175 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   VAL B 180 " --> pdb=" O   LEU B 176 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ILE B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   ASN B 182 " --> pdb=" O   VAL B 178 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   TYR B 188 " --> pdb=" O   VAL B 184 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLN B 190 " --> pdb=" O   SER B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 195
    Processing helix  chain 'B' and resid 201 through 251
      removed outlier: 3.959A  pdb=" N   ASP B 240 " --> pdb=" O   ARG B 236 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   TYR B 245 " --> pdb=" O   VAL B 241 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ILE B 246 " --> pdb=" O   ILE B 242 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   PHE B 250 " --> pdb=" O   ILE B 246 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   HIS B 251 " --> pdb=" O   LYS B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 260
      removed outlier: 4.186A  pdb=" N   PHE B 257 " --> pdb=" O   PRO B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 272
      removed outlier: 4.053A  pdb=" N   VAL B 266 " --> pdb=" O   THR B 262 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ARG B 268 " --> pdb=" O   GLU B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 304
      removed outlier: 5.005A  pdb=" N   SER B 291 " --> pdb=" O   PHE B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 311
    Processing helix  chain 'B' and resid 314 through 326
      removed outlier: 4.044A  pdb=" N   TYR B 318 " --> pdb=" O   ALA B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 353
      removed outlier: 4.078A  pdb=" N   LYS B 331 " --> pdb=" O   LYS B 327 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   ASP B 335 " --> pdb=" O   LYS B 331 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ALA B 339 " --> pdb=" O   ASP B 335 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   GLY B 353 " --> pdb=" O   GLU B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 361
      removed outlier: 3.871A  pdb=" N   ILE B 357 " --> pdb=" O   GLY B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 417
      removed outlier: 3.603A  pdb=" N   ARG B 366 " --> pdb=" O   SER B 362 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ASP B 376 " --> pdb=" O   LYS B 372 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   TYR B 377 " --> pdb=" O   GLU B 373 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU B 378 " --> pdb=" O   PHE B 374 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA B 387 " --> pdb=" O   THR B 383 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   LYS B 395 " --> pdb=" O   GLN B 391 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   LYS B 396 " --> pdb=" O   LYS B 392 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   VAL B 397 " --> pdb=" O   ALA B 393 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ILE B 406 " --> pdb=" O   LEU B 402 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU B 407 " --> pdb=" O   ASN B 403 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   VAL B 412 " --> pdb=" O   TRP B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 420 through 444
      removed outlier: 3.855A  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 460
      removed outlier: 3.580A  pdb=" N   LEU B 448 " --> pdb=" O   LEU B 444 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL B 453 " --> pdb=" O   GLN B 449 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLU B 460 " --> pdb=" O   ASN B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 532
      removed outlier: 4.096A  pdb=" N   MET B 530 " --> pdb=" O   LEU B 526 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   VAL B 531 " --> pdb=" O   ALA B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 552 through 559
      removed outlier: 3.510A  pdb=" N   LEU B 556 " --> pdb=" O   ASP B 552 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 579
      removed outlier: 3.875A  pdb=" N   ASN B 577 " --> pdb=" O   THR B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 588 through 598
      removed outlier: 3.652A  pdb=" N   ALA B 598 " --> pdb=" O   ALA B 594 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 638
      removed outlier: 3.945A  pdb=" N   THR B 638 " --> pdb=" O   ARG B 634 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 653 through 665
      removed outlier: 3.758A  pdb=" N   ILE B 665 " --> pdb=" O   VAL B 661 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 677 through 684
      removed outlier: 4.300A  pdb=" N   ALA B 681 " --> pdb=" O   ARG B 677 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   GLU B 682 " --> pdb=" O   LEU B 678 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   ARG B 683 " --> pdb=" O   THR B 679 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 700 through 708
      removed outlier: 3.876A  pdb=" N   GLY B 708 " --> pdb=" O   LEU B 704 " (cutoff:3.500A)
    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: 5.818A  pdb=" N   SER A 501 " --> pdb=" O   TYR A 491 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   TYR A 491 " --> pdb=" O   SER A 501 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   PHE A 486 " --> pdb=" O   SER A 542 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   SER A 542 " --> pdb=" O   PHE A 486 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   GLN A 488 " --> pdb=" O   GLU A 540 " (cutoff:3.500A)
      removed outlier: 4.880A  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: 6.026A  pdb=" N   ASN A 561 " --> pdb=" O   ILE A 644 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE A 672 " --> pdb=" O   ILE A 643 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   VAL A 513 " --> pdb=" O   PHE A 673 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   LYS A 512 " --> pdb=" O   LYS A 686 " (cutoff:3.500A)
      removed outlier: 8.239A  pdb=" N   VAL A 688 " --> pdb=" O   LYS A 512 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   ALA A 514 " --> pdb=" O   VAL A 688 " (cutoff:3.500A)
      removed outlier: 7.869A  pdb=" N   LEU A 690 " --> pdb=" O   ALA A 514 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   VAL A 516 " --> pdb=" O   LEU A 690 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   VAL A 687 " --> pdb=" O   GLU A 698 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   GLU A 698 " --> pdb=" O   VAL A 687 " (cutoff:3.500A)
      removed outlier: 6.582A  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: 5.935A  pdb=" N   SER B 501 " --> pdb=" O   TYR B 491 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   TYR B 491 " --> pdb=" O   SER B 501 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ILE B 503 " --> pdb=" O   VAL B 489 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   SER B 542 " --> pdb=" O   THR B 485 " (cutoff:3.500A)
      removed outlier: 4.903A  pdb=" N   VAL B 489 " --> pdb=" O   GLN B 538 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   GLN B 538 " --> pdb=" O   VAL B 489 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 560 through 561
      removed outlier: 5.822A  pdb=" N   ASN B 561 " --> pdb=" O   ILE B 644 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ILE B 643 " --> pdb=" O   THR B 670 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE B 672 " --> pdb=" O   ILE B 643 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LYS B 686 " --> pdb=" O   LYS B 512 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLY B 699 " --> pdb=" O   VAL B 687 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   GLU B 697 " --> pdb=" O   VAL B 689 " (cutoff:3.500A)

    475 hydrogen bonds defined for protein.
    1416 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.39

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1709
        1.33 -     1.45: 2015
        1.45 -     1.57: 5260
        1.57 -     1.70: 10
        1.70 -     1.82: 56
  Bond restraints: 9050
  Sorted by residual:
  bond pdb=" O5' ATP B 801 "
       pdb=" PA  ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.579  1.672 -0.093 1.10e-02 8.26e+03 7.14e+01
  bond pdb=" O5' ATP A 801 "
       pdb=" PA  ATP A 801 "
    ideal  model  delta    sigma   weight residual
    1.579  1.671 -0.092 1.10e-02 8.26e+03 7.01e+01
  bond pdb=" C2  ATP A 801 "
       pdb=" N1  ATP A 801 "
    ideal  model  delta    sigma   weight residual
    1.334  1.415 -0.081 1.00e-02 1.00e+04 6.53e+01
  bond pdb=" C2  ATP B 801 "
       pdb=" N1  ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.334  1.415 -0.081 1.00e-02 1.00e+04 6.49e+01
  bond pdb=" C5  ATP B 801 "
       pdb=" C6  ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.409  1.340  0.069 1.00e-02 1.00e+04 4.72e+01
  ... (remaining 9045 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.95: 11719
        2.95 -     5.90: 406
        5.90 -     8.85: 100
        8.85 -    11.80: 39
       11.80 -    14.75: 14
  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  123.40   13.43 1.00e+00 1.00e+00 1.80e+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  123.41   13.42 1.00e+00 1.00e+00 1.80e+02
  angle pdb=" PB  ATP A 801 "
        pdb=" O3B ATP A 801 "
        pdb=" PG  ATP A 801 "
      ideal   model   delta    sigma   weight residual
     139.87  127.31   12.56 1.00e+00 1.00e+00 1.58e+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  127.34   12.53 1.00e+00 1.00e+00 1.57e+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  117.83   10.86 1.00e+00 1.00e+00 1.18e+02
  ... (remaining 12273 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.20: 4896
       17.20 -    34.39: 495
       34.39 -    51.59: 100
       51.59 -    68.79: 20
       68.79 -    85.99: 7
  Dihedral angle restraints: 5518
    sinusoidal: 2224
      harmonic: 3294
  Sorted by residual:
  dihedral pdb=" CA  GLU A 349 "
           pdb=" C   GLU A 349 "
           pdb=" N   ASP A 350 "
           pdb=" CA  ASP A 350 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.99   27.01     0      5.00e+00 4.00e-02 2.92e+01
  dihedral pdb=" CA  LEU B 444 "
           pdb=" C   LEU B 444 "
           pdb=" N   GLN B 445 "
           pdb=" CA  GLN B 445 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.79  -26.21     0      5.00e+00 4.00e-02 2.75e+01
  dihedral pdb=" C   THR A 613 "
           pdb=" N   THR A 613 "
           pdb=" CA  THR A 613 "
           pdb=" CB  THR A 613 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -109.05  -12.95     0      2.50e+00 1.60e-01 2.68e+01
  ... (remaining 5515 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.128: 1409
       0.128 -    0.256: 82
       0.256 -    0.383: 6
       0.383 -    0.511: 0
       0.511 -    0.639: 1
  Chirality restraints: 1498
  Sorted by residual:
  chirality pdb=" CB  ILE A 158 "
            pdb=" CA  ILE A 158 "
            pdb=" CG1 ILE A 158 "
            pdb=" CG2 ILE A 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.01    0.64 2.00e-01 2.50e+01 1.02e+01
  chirality pdb=" CB  VAL A 531 "
            pdb=" CA  VAL A 531 "
            pdb=" CG1 VAL A 531 "
            pdb=" CG2 VAL A 531 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.77e+00
  chirality pdb=" CB  ILE A 674 "
            pdb=" CA  ILE A 674 "
            pdb=" CG1 ILE A 674 "
            pdb=" CG2 ILE A 674 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.30 2.00e-01 2.50e+01 2.19e+00
  ... (remaining 1495 not shown)

  Planarity restraints: 1522
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 514 "   -0.018 2.00e-02 2.50e+03   3.65e-02 1.33e+01
        pdb=" C   ALA A 514 "    0.063 2.00e-02 2.50e+03
        pdb=" O   ALA A 514 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   PHE A 515 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 331 "   -0.017 2.00e-02 2.50e+03   3.47e-02 1.20e+01
        pdb=" C   LYS B 331 "    0.060 2.00e-02 2.50e+03
        pdb=" O   LYS B 331 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   MET B 332 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 587 "   -0.013 2.00e-02 2.50e+03   2.66e-02 7.09e+00
        pdb=" C   THR A 587 "    0.046 2.00e-02 2.50e+03
        pdb=" O   THR A 587 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLN A 588 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1519 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 76
        2.54 -     3.13: 6510
        3.13 -     3.72: 14599
        3.72 -     4.31: 19032
        4.31 -     4.90: 30072
  Nonbonded interactions: 70289
  Sorted by model distance:
  nonbonded pdb=" O2B ATP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     1.952 2.170
  nonbonded pdb=" O2B ATP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     1.953 2.170
  nonbonded pdb=" NE2 GLN A 647 "
            pdb=" NE2 HIS A 676 "
     model   vdw
     2.042 3.200
  nonbonded pdb=" O3G ATP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     2.090 2.170
  nonbonded pdb=" O3G ATP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     2.090 2.170
  ... (remaining 70284 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.510
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.630
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
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   0.208   9051  Z= 0.491
  Angle     :  1.456  14.748  12278  Z= 0.796
  Chirality :  0.067   0.639   1498
  Planarity :  0.007   0.076   1522
  Dihedral  : 14.726  85.987   3394
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  :  5.97 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  0.91 %
    Favored  : 98.79 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.62 (0.20), residues: 1122
  helix: -2.23 (0.16), residues: 672
  sheet: -0.22 (1.13), residues: 24
  loop : -2.61 (0.24), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG B 627 
 TYR   0.023   0.002   TYR A 384 
 PHE   0.028   0.002   PHE A 374 
 TRP   0.013   0.003   TRP B 408 
 HIS   0.005   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00683 ( 9050)
  covalent geometry    : angle       1.45647 (12278)
  hydrogen bonds       : bond        0.14655 (  475)
  hydrogen bonds       : angle       6.92546 ( 1416)
  Misc. bond           : bond        0.20807 (    1)

*********************** 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
  140 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 137
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 ILE cc_start: 0.9638 (pt) cc_final: 0.9272 (mm)
REVERT: A  526 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9046 (tp)
REVERT: A  649 THR cc_start: 0.8848 (p) cc_final: 0.8397 (t)
REVERT: B  269 PHE cc_start: 0.9310 (t80) cc_final: 0.9099 (t80)
REVERT: B  308 PHE cc_start: 0.8864 (t80) cc_final: 0.8593 (t80)
REVERT: B  326 MET cc_start: 0.5150 (ptt) cc_final: 0.4269 (ptt)
REVERT: B  484 MET cc_start: 0.8908 (tpt) cc_final: 0.8481 (tpp)
  outliers start: 3
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0838
  time to fit residues: 17.2131
Evaluate side-chains
  94 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.0270
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    9.9990
   overall best weight:    4.4046

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 455 ASN
A 488 GLN
** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 251 HIS
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 571 ASN
B 628 GLN
** B 676 HIS ** 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 = 0.3808 r_free = 0.3808 target = 0.084988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.072990 restraints weight = 70198.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.074522 restraints weight = 42394.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.075608 restraints weight = 28819.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.076380 restraints weight = 21149.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.076969 restraints weight = 16450.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9051  Z= 0.185
  Angle     :  0.718   7.255  12278  Z= 0.378
  Chirality :  0.042   0.228   1498
  Planarity :  0.005   0.045   1522
  Dihedral  :  8.603  82.557   1280
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.90 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  7.68 %
    Favored  : 92.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.60 (0.23), residues: 1122
  helix: -0.51 (0.19), residues: 674
  sheet:  0.03 (1.21), residues: 24
  loop : -1.93 (0.26), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 627 
 TYR   0.016   0.002   TYR A 562 
 PHE   0.031   0.002   PHE B 309 
 TRP   0.002   0.000   TRP A 408 
 HIS   0.007   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 9050)
  covalent geometry    : angle       0.71842 (12278)
  hydrogen bonds       : bond        0.05034 (  475)
  hydrogen bonds       : angle       4.82303 ( 1416)
  Misc. bond           : bond        0.00148 (    1)

*********************** 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
  120 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  409 MET cc_start: 0.9121 (tmm) cc_final: 0.8807 (tmm)
REVERT: A  530 MET cc_start: 0.9270 (mpp) cc_final: 0.8997 (mpp)
REVERT: A  607 MET cc_start: 0.7611 (tmm) cc_final: 0.7280 (tmm)
REVERT: B  269 PHE cc_start: 0.9810 (t80) cc_final: 0.9517 (t80)
REVERT: B  409 MET cc_start: 0.8704 (ppp) cc_final: 0.8332 (ppp)
REVERT: B  559 TYR cc_start: 0.9023 (p90) cc_final: 0.8762 (p90)
  outliers start: 2
  outliers final: 2
  residues processed: 120
  average time/residue: 0.0744
  time to fit residues: 13.6200
Evaluate side-chains
  89 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 87
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 29 optimal weight:    6.9990
   chunk 42 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 59 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 101 optimal weight:   10.0000
   chunk 95 optimal weight:    5.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 628 GLN
** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 248 HIS
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 647 GLN
B 676 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.055511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.044364 restraints weight = 69920.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.045562 restraints weight = 51243.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.046484 restraints weight = 40396.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.047205 restraints weight = 33423.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.047762 restraints weight = 28669.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9051  Z= 0.184
  Angle     :  0.713   7.891  12278  Z= 0.375
  Chirality :  0.043   0.199   1498
  Planarity :  0.004   0.037   1522
  Dihedral  :  7.966  88.799   1280
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.88 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  5.96 %
    Favored  : 93.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.12 (0.24), residues: 1122
  helix: -0.09 (0.20), residues: 674
  sheet:  0.14 (1.23), residues: 24
  loop : -1.78 (0.27), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 593 
 TYR   0.023   0.002   TYR B 493 
 PHE   0.031   0.002   PHE B 309 
 TRP   0.005   0.001   TRP B 408 
 HIS   0.006   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 9050)
  covalent geometry    : angle       0.71319 (12278)
  hydrogen bonds       : bond        0.04906 (  475)
  hydrogen bonds       : angle       4.71083 ( 1416)
  Misc. bond           : bond        0.00129 (    1)

*********************** 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
  113 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 HIS cc_start: 0.9402 (m-70) cc_final: 0.9179 (m-70)
REVERT: A  310 MET cc_start: 0.4079 (ttt) cc_final: 0.3388 (tpt)
REVERT: A  409 MET cc_start: 0.9250 (tmm) cc_final: 0.8758 (ppp)
REVERT: A  559 TYR cc_start: 0.9035 (p90) cc_final: 0.8696 (p90)
REVERT: A  607 MET cc_start: 0.7903 (tmm) cc_final: 0.7472 (tmm)
REVERT: B  196 TYR cc_start: 0.8070 (m-80) cc_final: 0.7850 (m-80)
REVERT: B  201 MET cc_start: 0.2290 (mpp) cc_final: 0.1952 (mpp)
REVERT: B  269 PHE cc_start: 0.9693 (t80) cc_final: 0.9422 (t80)
REVERT: B  308 PHE cc_start: 0.9221 (t80) cc_final: 0.8958 (t80)
REVERT: B  310 MET cc_start: 0.5574 (ptp) cc_final: 0.5352 (ptm)
REVERT: B  357 ILE cc_start: 0.9818 (mm) cc_final: 0.9610 (tp)
REVERT: B  409 MET cc_start: 0.8786 (ppp) cc_final: 0.8424 (ppp)
  outliers start: 1
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0711
  time to fit residues: 12.5966
Evaluate side-chains
  89 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 52 optimal weight:    8.9990
   chunk 64 optimal weight:    6.9990
   chunk 69 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 39 optimal weight:    0.4980
   chunk 60 optimal weight:    0.4980
   chunk 45 optimal weight:    9.9990
   chunk 76 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 108 optimal weight:    8.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 GLN
** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 440 ASN
B 571 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.056889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.045632 restraints weight = 69918.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.046846 restraints weight = 51283.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.047796 restraints weight = 40331.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.048516 restraints weight = 33336.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.049098 restraints weight = 28631.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.3082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9051  Z= 0.129
  Angle     :  0.665   8.188  12278  Z= 0.340
  Chirality :  0.042   0.193   1498
  Planarity :  0.004   0.041   1522
  Dihedral  :  7.150  87.578   1280
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.90 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.64 (0.25), residues: 1122
  helix:  0.32 (0.20), residues: 668
  sheet:  0.34 (1.20), residues: 24
  loop : -1.62 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 557 
 TYR   0.009   0.001   TYR A 559 
 PHE   0.029   0.001   PHE B 309 
 TRP   0.005   0.001   TRP B 408 
 HIS   0.006   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9050)
  covalent geometry    : angle       0.66468 (12278)
  hydrogen bonds       : bond        0.04659 (  475)
  hydrogen bonds       : angle       4.43695 ( 1416)
  Misc. bond           : bond        0.00159 (    1)

*********************** 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
  115 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 HIS cc_start: 0.9370 (m-70) cc_final: 0.9153 (m-70)
REVERT: A  310 MET cc_start: 0.4095 (ttt) cc_final: 0.3333 (tpt)
REVERT: A  409 MET cc_start: 0.9153 (tmm) cc_final: 0.8653 (ppp)
REVERT: A  607 MET cc_start: 0.7880 (tmm) cc_final: 0.7299 (tmm)
REVERT: B  201 MET cc_start: 0.2189 (mpp) cc_final: 0.1856 (mpp)
REVERT: B  269 PHE cc_start: 0.9704 (t80) cc_final: 0.9448 (t80)
REVERT: B  308 PHE cc_start: 0.9192 (t80) cc_final: 0.8947 (t80)
REVERT: B  310 MET cc_start: 0.5517 (ptp) cc_final: 0.5248 (ptm)
REVERT: B  357 ILE cc_start: 0.9800 (mm) cc_final: 0.9578 (tp)
REVERT: B  409 MET cc_start: 0.8645 (ppp) cc_final: 0.8366 (ppp)
REVERT: B  484 MET cc_start: 0.9003 (tpt) cc_final: 0.8454 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0705
  time to fit residues: 12.6001
Evaluate side-chains
  94 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 82 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 78 optimal weight:    8.9990
   chunk 13 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 95 optimal weight:    1.9990
   chunk 109 optimal weight:   20.0000
   chunk 32 optimal weight:    5.9990
   chunk 91 optimal weight:   30.0000
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 571 ASN ** 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 = 0.3293 r_free = 0.3293 target = 0.055540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.044952 restraints weight = 70573.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.046080 restraints weight = 52318.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.046947 restraints weight = 41474.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.047631 restraints weight = 34487.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.048191 restraints weight = 29613.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.3450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9051  Z= 0.156
  Angle     :  0.683   8.554  12278  Z= 0.355
  Chirality :  0.042   0.191   1498
  Planarity :  0.004   0.037   1522
  Dihedral  :  6.662  83.186   1280
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.70 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.04 %
    Favored  : 95.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.25), residues: 1122
  helix:  0.39 (0.20), residues: 668
  sheet:  0.41 (1.20), residues: 24
  loop : -1.53 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 557 
 TYR   0.014   0.001   TYR A 491 
 PHE   0.028   0.002   PHE B 309 
 TRP   0.005   0.001   TRP B 408 
 HIS   0.008   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 9050)
  covalent geometry    : angle       0.68303 (12278)
  hydrogen bonds       : bond        0.04680 (  475)
  hydrogen bonds       : angle       4.57364 ( 1416)
  Misc. bond           : bond        0.00053 (    1)

*********************** 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
  109 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 HIS cc_start: 0.9372 (m-70) cc_final: 0.9154 (m-70)
REVERT: A  310 MET cc_start: 0.4523 (ttt) cc_final: 0.3608 (tpt)
REVERT: A  409 MET cc_start: 0.9265 (tmm) cc_final: 0.8770 (ppp)
REVERT: A  607 MET cc_start: 0.7980 (tmm) cc_final: 0.7269 (tmm)
REVERT: B  269 PHE cc_start: 0.9721 (t80) cc_final: 0.9474 (t80)
REVERT: B  308 PHE cc_start: 0.9219 (t80) cc_final: 0.8972 (t80)
REVERT: B  310 MET cc_start: 0.5776 (ptp) cc_final: 0.5516 (ptm)
REVERT: B  357 ILE cc_start: 0.9806 (mm) cc_final: 0.9553 (tp)
REVERT: B  409 MET cc_start: 0.8647 (ppp) cc_final: 0.8360 (ppp)
  outliers start: 1
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0724
  time to fit residues: 12.2787
Evaluate side-chains
  91 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 33 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 71 optimal weight:    4.9990
   chunk 98 optimal weight:    6.9990
   chunk 23 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 41 optimal weight:    4.9990
   chunk 64 optimal weight:    8.9990
   chunk 68 optimal weight:    2.9990
   chunk 66 optimal weight:    9.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 459 ASN
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.054724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.044138 restraints weight = 71673.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.045265 restraints weight = 53012.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.046114 restraints weight = 42003.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.046784 restraints weight = 34970.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.047306 restraints weight = 30074.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.3810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9051  Z= 0.165
  Angle     :  0.704   8.264  12278  Z= 0.365
  Chirality :  0.043   0.193   1498
  Planarity :  0.004   0.039   1522
  Dihedral  :  6.715  84.446   1280
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.61 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  3.74 %
    Favored  : 96.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.25), residues: 1122
  helix:  0.47 (0.20), residues: 666
  sheet:  0.67 (1.21), residues: 24
  loop : -1.50 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 557 
 TYR   0.013   0.001   TYR A 559 
 PHE   0.028   0.002   PHE B 309 
 TRP   0.007   0.001   TRP B 408 
 HIS   0.008   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9050)
  covalent geometry    : angle       0.70429 (12278)
  hydrogen bonds       : bond        0.04766 (  475)
  hydrogen bonds       : angle       4.64125 ( 1416)
  Misc. bond           : bond        0.00089 (    1)

*********************** 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
  112 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 110
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 MET cc_start: 0.4961 (ttt) cc_final: 0.3932 (tpt)
REVERT: A  404 VAL cc_start: 0.8920 (m) cc_final: 0.8720 (p)
REVERT: A  409 MET cc_start: 0.9277 (tmm) cc_final: 0.8772 (ppp)
REVERT: A  607 MET cc_start: 0.7946 (tmm) cc_final: 0.7184 (tmm)
REVERT: B  269 PHE cc_start: 0.9705 (t80) cc_final: 0.9479 (t80)
REVERT: B  308 PHE cc_start: 0.9223 (t80) cc_final: 0.8994 (t80)
REVERT: B  310 MET cc_start: 0.6080 (ptp) cc_final: 0.5737 (ptm)
REVERT: B  357 ILE cc_start: 0.9805 (mm) cc_final: 0.9559 (tp)
REVERT: B  409 MET cc_start: 0.8615 (ppp) cc_final: 0.8377 (ppp)
  outliers start: 2
  outliers final: 1
  residues processed: 112
  average time/residue: 0.0673
  time to fit residues: 11.6617
Evaluate side-chains
  91 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 106 optimal weight:    9.9990
   chunk 111 optimal weight:    8.9990
   chunk 11 optimal weight:    8.9990
   chunk 41 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0020
   chunk 89 optimal weight:    6.9990
   chunk 6 optimal weight:    0.3980
   overall best weight:    0.8790

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

Flipped N/Q/H residues before XYZ refinement:
** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 248 HIS
** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.057577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.046130 restraints weight = 67589.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.047348 restraints weight = 50021.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.048279 restraints weight = 39553.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.049004 restraints weight = 32863.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.049580 restraints weight = 28244.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.3724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9051  Z= 0.123
  Angle     :  0.685  10.326  12278  Z= 0.341
  Chirality :  0.042   0.168   1498
  Planarity :  0.003   0.038   1522
  Dihedral  :  6.434  81.728   1280
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.37 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.25), residues: 1122
  helix:  0.66 (0.20), residues: 670
  sheet:  0.78 (1.19), residues: 24
  loop : -1.46 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 260 
 TYR   0.017   0.001   TYR A 559 
 PHE   0.027   0.001   PHE B 309 
 TRP   0.007   0.001   TRP A 408 
 HIS   0.007   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 9050)
  covalent geometry    : angle       0.68537 (12278)
  hydrogen bonds       : bond        0.04440 (  475)
  hydrogen bonds       : angle       4.33728 ( 1416)
  Misc. bond           : bond        0.00054 (    1)

*********************** 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
  115 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 PHE cc_start: 0.9174 (t80) cc_final: 0.8890 (t80)
REVERT: A  310 MET cc_start: 0.4189 (ttt) cc_final: 0.3233 (tpt)
REVERT: A  409 MET cc_start: 0.9179 (tmm) cc_final: 0.8661 (ppp)
REVERT: A  607 MET cc_start: 0.7845 (tmm) cc_final: 0.7526 (tmm)
REVERT: B  196 TYR cc_start: 0.8246 (m-80) cc_final: 0.7875 (m-80)
REVERT: B  229 LEU cc_start: 0.9723 (mm) cc_final: 0.9445 (pp)
REVERT: B  269 PHE cc_start: 0.9702 (t80) cc_final: 0.9460 (t80)
REVERT: B  310 MET cc_start: 0.5756 (ptp) cc_final: 0.5429 (ptm)
REVERT: B  357 ILE cc_start: 0.9783 (mm) cc_final: 0.9520 (tp)
REVERT: B  530 MET cc_start: 0.9166 (mpp) cc_final: 0.8873 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0691
  time to fit residues: 12.3345
Evaluate side-chains
  91 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    7.9990
   chunk 84 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 399 HIS
** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 248 HIS
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.054160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.043755 restraints weight = 72060.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.044872 restraints weight = 53320.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.045742 restraints weight = 42241.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.046394 restraints weight = 35008.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.046913 restraints weight = 30142.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.4184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9051  Z= 0.187
  Angle     :  0.736   8.768  12278  Z= 0.380
  Chirality :  0.044   0.208   1498
  Planarity :  0.004   0.050   1522
  Dihedral  :  6.715  82.853   1280
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 17.58
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  6.24 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.25), residues: 1122
  helix:  0.60 (0.20), residues: 666
  sheet:  0.59 (1.18), residues: 24
  loop : -1.38 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 557 
 TYR   0.022   0.002   TYR B 493 
 PHE   0.025   0.002   PHE A 308 
 TRP   0.005   0.001   TRP B 408 
 HIS   0.007   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 9050)
  covalent geometry    : angle       0.73624 (12278)
  hydrogen bonds       : bond        0.04669 (  475)
  hydrogen bonds       : angle       4.68476 ( 1416)
  Misc. bond           : bond        0.00136 (    1)

*********************** 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
  108 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 MET cc_start: 0.4830 (ttt) cc_final: 0.3753 (ptm)
REVERT: A  357 ILE cc_start: 0.9781 (mp) cc_final: 0.9408 (tp)
REVERT: A  607 MET cc_start: 0.8034 (tmm) cc_final: 0.7711 (tmm)
REVERT: B  196 TYR cc_start: 0.8288 (m-80) cc_final: 0.7982 (m-80)
REVERT: B  269 PHE cc_start: 0.9693 (t80) cc_final: 0.9477 (t80)
REVERT: B  308 PHE cc_start: 0.9139 (t80) cc_final: 0.8892 (t80)
REVERT: B  310 MET cc_start: 0.5541 (ptp) cc_final: 0.5207 (ptm)
REVERT: B  357 ILE cc_start: 0.9792 (mm) cc_final: 0.9554 (tp)
REVERT: B  409 MET cc_start: 0.8577 (ppp) cc_final: 0.8359 (ppp)
REVERT: B  484 MET cc_start: 0.8938 (tpt) cc_final: 0.8703 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0743
  time to fit residues: 12.4689
Evaluate side-chains
  91 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 106 optimal weight:    6.9990
   chunk 65 optimal weight:    8.9990
   chunk 78 optimal weight:    4.9990
   chunk 12 optimal weight:   20.0000
   chunk 20 optimal weight:    0.0980
   chunk 96 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 104 optimal weight:    6.9990
   overall best weight:    3.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 248 HIS
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.055039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.044385 restraints weight = 69615.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.045521 restraints weight = 51479.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.046389 restraints weight = 40784.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.047058 restraints weight = 33913.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.047609 restraints weight = 29162.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9051  Z= 0.149
  Angle     :  0.726  10.577  12278  Z= 0.370
  Chirality :  0.044   0.187   1498
  Planarity :  0.004   0.039   1522
  Dihedral  :  6.676  82.930   1280
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 14.71
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.44 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.25), residues: 1122
  helix:  0.56 (0.20), residues: 670
  sheet:  0.80 (1.08), residues: 26
  loop : -1.37 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 557 
 TYR   0.017   0.001   TYR A 559 
 PHE   0.028   0.002   PHE B 309 
 TRP   0.006   0.001   TRP B 408 
 HIS   0.007   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9050)
  covalent geometry    : angle       0.72584 (12278)
  hydrogen bonds       : bond        0.04599 (  475)
  hydrogen bonds       : angle       4.64141 ( 1416)
  Misc. bond           : bond        0.00064 (    1)

*********************** 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
  108 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 PHE cc_start: 0.9133 (t80) cc_final: 0.8745 (t80)
REVERT: A  310 MET cc_start: 0.4649 (ttt) cc_final: 0.3929 (tpt)
REVERT: A  607 MET cc_start: 0.8073 (tmm) cc_final: 0.7762 (tmm)
REVERT: B  196 TYR cc_start: 0.8270 (m-80) cc_final: 0.7867 (m-80)
REVERT: B  269 PHE cc_start: 0.9683 (t80) cc_final: 0.9467 (t80)
REVERT: B  310 MET cc_start: 0.5422 (ptp) cc_final: 0.5119 (ptm)
REVERT: B  357 ILE cc_start: 0.9792 (mm) cc_final: 0.9520 (tp)
REVERT: B  409 MET cc_start: 0.8513 (ppp) cc_final: 0.8308 (ppp)
REVERT: B  530 MET cc_start: 0.9110 (mpp) cc_final: 0.8903 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0717
  time to fit residues: 12.1015
Evaluate side-chains
  89 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    0.0470
   chunk 31 optimal weight:    0.9990
   chunk 99 optimal weight:    9.9990
   chunk 20 optimal weight:    0.2980
   chunk 39 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 96 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0970
   chunk 45 optimal weight:    0.6980
   chunk 81 optimal weight:    3.9990
   chunk 75 optimal weight:    9.9990
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 550 GLN
B 571 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.058561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.047302 restraints weight = 64631.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.048519 restraints weight = 48031.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.049463 restraints weight = 38053.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.050199 restraints weight = 31570.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.050791 restraints weight = 27108.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.4169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9051  Z= 0.130
  Angle     :  0.723  10.233  12278  Z= 0.359
  Chirality :  0.044   0.177   1498
  Planarity :  0.003   0.039   1522
  Dihedral  :  6.438  82.130   1280
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.37 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.25), residues: 1122
  helix:  0.63 (0.20), residues: 670
  sheet:  1.20 (1.10), residues: 26
  loop : -1.37 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 557 
 TYR   0.019   0.001   TYR A 559 
 PHE   0.026   0.001   PHE B 309 
 TRP   0.007   0.001   TRP A 408 
 HIS   0.007   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9050)
  covalent geometry    : angle       0.72333 (12278)
  hydrogen bonds       : bond        0.04335 (  475)
  hydrogen bonds       : angle       4.41067 ( 1416)
  Misc. bond           : bond        0.00000 (    1)

********************** 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
  114 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 LEU cc_start: 0.9467 (tp) cc_final: 0.9137 (tp)
REVERT: A  308 PHE cc_start: 0.9197 (t80) cc_final: 0.8937 (t80)
REVERT: A  310 MET cc_start: 0.4097 (ttt) cc_final: 0.3284 (tpt)
REVERT: A  409 MET cc_start: 0.9136 (tmm) cc_final: 0.8666 (ppp)
REVERT: A  607 MET cc_start: 0.7706 (tmm) cc_final: 0.7419 (tmm)
REVERT: A  615 LEU cc_start: 0.9534 (pp) cc_final: 0.9333 (pp)
REVERT: B  196 TYR cc_start: 0.8301 (m-80) cc_final: 0.7884 (m-80)
REVERT: B  269 PHE cc_start: 0.9704 (t80) cc_final: 0.9472 (t80)
REVERT: B  310 MET cc_start: 0.5114 (ptp) cc_final: 0.4883 (ptm)
REVERT: B  357 ILE cc_start: 0.9776 (mm) cc_final: 0.9482 (tp)
REVERT: B  384 TYR cc_start: 0.9309 (t80) cc_final: 0.8846 (t80)
REVERT: B  484 MET cc_start: 0.8858 (tpt) cc_final: 0.8605 (tpt)
REVERT: B  530 MET cc_start: 0.9193 (mpp) cc_final: 0.8867 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0690
  time to fit residues: 12.3247
Evaluate side-chains
  92 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 109 optimal weight:    6.9990
   chunk 97 optimal weight:    0.5980
   chunk 46 optimal weight:    6.9990
   chunk 88 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 111 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    4.1188

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

Flipped N/Q/H residues before XYZ refinement:
** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 550 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 = 0.3287 r_free = 0.3287 target = 0.054970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.044627 restraints weight = 70548.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.045712 restraints weight = 52732.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.046557 restraints weight = 42009.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.047210 restraints weight = 35061.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.047735 restraints weight = 30276.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.4458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9051  Z= 0.169
  Angle     :  0.733  11.081  12278  Z= 0.373
  Chirality :  0.044   0.177   1498
  Planarity :  0.004   0.043   1522
  Dihedral  :  6.594  80.399   1280
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.35 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.25), residues: 1122
  helix:  0.62 (0.20), residues: 670
  sheet:  0.96 (1.08), residues: 26
  loop : -1.39 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 457 
 TYR   0.019   0.001   TYR B 493 
 PHE   0.026   0.002   PHE B 309 
 TRP   0.005   0.001   TRP A 408 
 HIS   0.006   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 9050)
  covalent geometry    : angle       0.73335 (12278)
  hydrogen bonds       : bond        0.04411 (  475)
  hydrogen bonds       : angle       4.61687 ( 1416)
  Misc. bond           : bond        0.00090 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1454.13 seconds
wall clock time: 26 minutes 5.06 seconds (1565.06 seconds total)