Starting phenix.real_space_refine
on Thu Mar 13 17:52:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k7a_36936/03_2025/8k7a_36936.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k7a_36936/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k7a_36936/03_2025/8k7a_36936.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k7a_36936/03_2025/8k7a_36936.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k7a_36936/03_2025/8k7a_36936.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k7a_36936/03_2025/8k7a_36936.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8918
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 563, 4427
          Classifications: {'peptide': 563}
          Link IDs: {'PTRANS': 12, 'TRANS': 550}
    Chain: "B"
      Number of atoms: 4427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 563, 4427
          Classifications: {'peptide': 563}
          Link IDs: {'PTRANS': 12, 'TRANS': 550}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' 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: 5.37, per 1000 atoms: 0.60
  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: 2.40
  Conformation dependent library (CDL) restraints added in 983.4 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      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: 0.83
  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: 2.30

  Time building geometry restraints manager: 2.67 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.060
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.430
-------------------------------------------------------------------------------
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   0.093   9050  Z= 0.432
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.62 (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
 TRP   0.013   0.003   TRP B 408 
 HIS   0.005   0.001   HIS A 490 
 PHE   0.028   0.002   PHE A 374 
 TYR   0.023   0.002   TYR A 384 
 ARG   0.018   0.001   ARG B 627 

*********************** 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  : 0.956 
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: 0.1702
  time to fit residues: 34.8175
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  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 84 optimal weight:    7.9990
   chunk 47 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 57 optimal weight:    9.9990
   chunk 45 optimal weight:    0.0170
   chunk 87 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   chunk 101 optimal weight:    0.8980
   overall best weight:    1.1222

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

Flipped N/Q/H residues before XYZ refinement:
A 455 ASN
** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 628 GLN
** B 676 HIS ** 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 = 0.3922 r_free = 0.3922 target = 0.092421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.079691 restraints weight = 66790.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.081351 restraints weight = 40436.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.082512 restraints weight = 27492.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9050  Z= 0.143
  Angle     :  0.670   7.210  12278  Z= 0.340
  Chirality :  0.041   0.227   1498
  Planarity :  0.004   0.046   1522
  Dihedral  :  8.481  75.048   1280
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.28 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  6.57 %
    Favored  : 93.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.23), residues: 1122
  helix: -0.64 (0.19), residues: 678
  sheet: -0.01 (1.18), residues: 24
  loop : -2.10 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP A 408 
 HIS   0.004   0.001   HIS A 490 
 PHE   0.031   0.001   PHE B 309 
 TYR   0.012   0.001   TYR A 559 
 ARG   0.005   0.000   ARG B 627 

*********************** 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
  129 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  409 MET cc_start: 0.9040 (tmm) cc_final: 0.8690 (tmm)
REVERT: A  607 MET cc_start: 0.7300 (tmm) cc_final: 0.7014 (tmm)
REVERT: B  269 PHE cc_start: 0.9805 (t80) cc_final: 0.9518 (t80)
REVERT: B  308 PHE cc_start: 0.9167 (t80) cc_final: 0.8817 (t80)
REVERT: B  371 ASP cc_start: 0.9818 (t0) cc_final: 0.9497 (m-30)
REVERT: B  419 MET cc_start: 0.7610 (tpt) cc_final: 0.7196 (tpp)
REVERT: B  530 MET cc_start: 0.9235 (mpp) cc_final: 0.9024 (mpp)
  outliers start: 1
  outliers final: 1
  residues processed: 129
  average time/residue: 0.1588
  time to fit residues: 30.6444
Evaluate side-chains
  95 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 53 optimal weight:    0.4980
   chunk 87 optimal weight:    8.9990
   chunk 71 optimal weight:    4.9990
   chunk 65 optimal weight:    9.9990
   chunk 102 optimal weight:    8.9990
   chunk 46 optimal weight:    0.4980
   chunk 78 optimal weight:    9.9990
   chunk 95 optimal weight:    7.9990
   chunk 3 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   overall best weight:    3.7986

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.059668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.046514 restraints weight = 66430.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.048060 restraints weight = 45747.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.049223 restraints weight = 34634.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9050  Z= 0.208
  Angle     :  0.689   7.457  12278  Z= 0.358
  Chirality :  0.042   0.184   1498
  Planarity :  0.004   0.037   1522
  Dihedral  :  8.311  87.708   1280
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.99 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  5.25 %
    Favored  : 94.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.24), residues: 1122
  helix: -0.09 (0.20), residues: 676
  sheet:  0.33 (1.24), residues: 24
  loop : -1.86 (0.27), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 408 
 HIS   0.004   0.001   HIS A 490 
 PHE   0.028   0.002   PHE B 309 
 TYR   0.018   0.002   TYR A 493 
 ARG   0.004   0.001   ARG A 593 

*********************** 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
  114 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 ILE cc_start: 0.9652 (pt) cc_final: 0.9334 (mm)
REVERT: A  251 HIS cc_start: 0.9452 (m-70) cc_final: 0.9215 (m170)
REVERT: A  310 MET cc_start: 0.3762 (ttt) cc_final: 0.3177 (tpt)
REVERT: A  409 MET cc_start: 0.9143 (tmm) cc_final: 0.8662 (ppp)
REVERT: A  559 TYR cc_start: 0.9025 (p90) cc_final: 0.8737 (p90)
REVERT: A  607 MET cc_start: 0.7833 (tmm) cc_final: 0.7345 (tmm)
REVERT: B  229 LEU cc_start: 0.9756 (mm) cc_final: 0.9494 (pp)
REVERT: B  269 PHE cc_start: 0.9732 (t80) cc_final: 0.9433 (t80)
REVERT: B  310 MET cc_start: 0.5427 (ptp) cc_final: 0.5202 (ptm)
REVERT: B  357 ILE cc_start: 0.9835 (mm) cc_final: 0.9632 (tp)
REVERT: B  409 MET cc_start: 0.8745 (ppp) cc_final: 0.8394 (ppp)
REVERT: B  528 LYS cc_start: 0.9777 (mmtt) cc_final: 0.9561 (mmtm)
REVERT: B  559 TYR cc_start: 0.8949 (p90) cc_final: 0.8733 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1553
  time to fit residues: 27.3475
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  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 80 optimal weight:    9.9990
   chunk 89 optimal weight:    7.9990
   chunk 66 optimal weight:    9.9990
   chunk 99 optimal weight:    4.9990
   chunk 40 optimal weight:    8.9990
   chunk 109 optimal weight:   20.0000
   chunk 108 optimal weight:   20.0000
   chunk 77 optimal weight:    0.9990
   chunk 98 optimal weight:    0.0010
   overall best weight:    4.1994

-------------------------------------------------------------------------------
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 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 248 HIS
B 440 ASN
** B 490 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**
** B 676 HIS ** 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 = 0.3298 r_free = 0.3298 target = 0.055695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.044476 restraints weight = 69375.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.045645 restraints weight = 51226.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.046546 restraints weight = 40596.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9050  Z= 0.211
  Angle     :  0.680   8.401  12278  Z= 0.354
  Chirality :  0.043   0.202   1498
  Planarity :  0.004   0.038   1522
  Dihedral  :  7.368  84.930   1280
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  6.15 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.24), residues: 1122
  helix:  0.21 (0.20), residues: 674
  sheet:  0.30 (1.21), residues: 24
  loop : -1.69 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 408 
 HIS   0.007   0.001   HIS A 490 
 PHE   0.030   0.002   PHE B 309 
 TYR   0.023   0.002   TYR A 493 
 ARG   0.007   0.001   ARG B 260 

*********************** 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  : 0.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 ILE cc_start: 0.9654 (pt) cc_final: 0.9331 (mm)
REVERT: A  251 HIS cc_start: 0.9396 (m-70) cc_final: 0.9171 (m-70)
REVERT: A  264 GLU cc_start: 0.8850 (pt0) cc_final: 0.8519 (pt0)
REVERT: A  310 MET cc_start: 0.4373 (ttt) cc_final: 0.3624 (tpt)
REVERT: A  409 MET cc_start: 0.9160 (tmm) cc_final: 0.8687 (ppp)
REVERT: A  607 MET cc_start: 0.7896 (tmm) cc_final: 0.7250 (tmm)
REVERT: B  196 TYR cc_start: 0.8160 (m-80) cc_final: 0.7943 (m-80)
REVERT: B  201 MET cc_start: 0.2463 (mpp) cc_final: 0.2076 (mpp)
REVERT: B  229 LEU cc_start: 0.9754 (mm) cc_final: 0.9495 (pp)
REVERT: B  269 PHE cc_start: 0.9715 (t80) cc_final: 0.9451 (t80)
REVERT: B  308 PHE cc_start: 0.9225 (t80) cc_final: 0.8970 (t80)
REVERT: B  310 MET cc_start: 0.5766 (ptp) cc_final: 0.5465 (ptm)
REVERT: B  357 ILE cc_start: 0.9813 (mm) cc_final: 0.9599 (tp)
REVERT: B  409 MET cc_start: 0.8730 (ppp) cc_final: 0.8425 (ppp)
REVERT: B  484 MET cc_start: 0.9092 (tpt) cc_final: 0.8627 (tpp)
REVERT: B  690 LEU cc_start: 0.9608 (tp) cc_final: 0.9133 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1547
  time to fit residues: 27.2444
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  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 105 optimal weight:   30.0000
   chunk 104 optimal weight:    4.9990
   chunk 100 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0570
   chunk 47 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    3.2106

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 490 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 = 0.3298 r_free = 0.3298 target = 0.055829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.044649 restraints weight = 68647.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.045839 restraints weight = 50693.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.046742 restraints weight = 40039.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9050  Z= 0.179
  Angle     :  0.664   8.153  12278  Z= 0.339
  Chirality :  0.042   0.187   1498
  Planarity :  0.004   0.037   1522
  Dihedral  :  6.861  89.459   1280
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.17 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  3.54 %
    Favored  : 96.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.25), residues: 1122
  helix:  0.45 (0.20), residues: 674
  sheet:  0.40 (1.20), residues: 24
  loop : -1.64 (0.27), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 408 
 HIS   0.007   0.001   HIS A 490 
 PHE   0.028   0.001   PHE B 309 
 TYR   0.015   0.001   TYR A 493 
 ARG   0.003   0.000   ARG B 457 

*********************** 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
  116 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 114
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 MET cc_start: 0.4332 (ttt) cc_final: 0.3456 (tpt)
REVERT: A  409 MET cc_start: 0.9176 (tmm) cc_final: 0.8709 (ppp)
REVERT: A  607 MET cc_start: 0.7867 (tmm) cc_final: 0.7141 (tmm)
REVERT: B  201 MET cc_start: 0.2420 (mpp) cc_final: 0.2047 (mpp)
REVERT: B  269 PHE cc_start: 0.9725 (t80) cc_final: 0.9469 (t80)
REVERT: B  308 PHE cc_start: 0.9231 (t80) cc_final: 0.8995 (t80)
REVERT: B  310 MET cc_start: 0.5736 (ptp) cc_final: 0.5444 (ptm)
REVERT: B  357 ILE cc_start: 0.9801 (mm) cc_final: 0.9573 (tp)
REVERT: B  409 MET cc_start: 0.8660 (ppp) cc_final: 0.8391 (ppp)
  outliers start: 2
  outliers final: 1
  residues processed: 116
  average time/residue: 0.2680
  time to fit residues: 47.7339
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  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 73 optimal weight:    9.9990
   chunk 32 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 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 = 0.3310 r_free = 0.3310 target = 0.056169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.045163 restraints weight = 69022.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.046321 restraints weight = 51310.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.047200 restraints weight = 40806.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.3494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9050  Z= 0.162
  Angle     :  0.667   9.067  12278  Z= 0.343
  Chirality :  0.042   0.171   1498
  Planarity :  0.003   0.037   1522
  Dihedral  :  6.701  88.129   1280
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.70 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.25), residues: 1122
  helix:  0.51 (0.20), residues: 674
  sheet:  0.57 (1.20), residues: 24
  loop : -1.61 (0.27), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 408 
 HIS   0.006   0.001   HIS A 490 
 PHE   0.028   0.001   PHE B 309 
 TYR   0.014   0.001   TYR A 559 
 ARG   0.003   0.000   ARG B 457 

*********************** 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
  113 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 1.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 GLU cc_start: 0.9362 (mp0) cc_final: 0.9049 (pm20)
REVERT: A  310 MET cc_start: 0.4549 (ttt) cc_final: 0.3611 (tpt)
REVERT: A  409 MET cc_start: 0.9199 (tmm) cc_final: 0.8740 (ppp)
REVERT: A  607 MET cc_start: 0.7845 (tmm) cc_final: 0.7049 (tmm)
REVERT: B  229 LEU cc_start: 0.9718 (mm) cc_final: 0.9469 (pp)
REVERT: B  269 PHE cc_start: 0.9720 (t80) cc_final: 0.9472 (t80)
REVERT: B  308 PHE cc_start: 0.9208 (t80) cc_final: 0.9007 (t80)
REVERT: B  310 MET cc_start: 0.5784 (ptp) cc_final: 0.5446 (ptm)
REVERT: B  357 ILE cc_start: 0.9791 (mm) cc_final: 0.9521 (tp)
REVERT: B  367 TYR cc_start: 0.9279 (t80) cc_final: 0.8661 (t80)
REVERT: B  409 MET cc_start: 0.8572 (ppp) cc_final: 0.8343 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1697
  time to fit residues: 29.9389
Evaluate side-chains
  90 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 110 optimal weight:   20.0000
   chunk 59 optimal weight:   20.0000
   chunk 31 optimal weight:    0.7980
   chunk 107 optimal weight:    0.0050
   chunk 66 optimal weight:    3.9990
   chunk 47 optimal weight:   10.0000
   chunk 24 optimal weight:    8.9990
   chunk 52 optimal weight:    5.9990
   chunk 96 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 56 optimal weight:   20.0000
   overall best weight:    2.9600

-------------------------------------------------------------------------------
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 490 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.055670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.044775 restraints weight = 69391.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.045922 restraints weight = 51514.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.046814 restraints weight = 40881.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.3687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9050  Z= 0.174
  Angle     :  0.689   9.490  12278  Z= 0.352
  Chirality :  0.043   0.176   1498
  Planarity :  0.004   0.037   1522
  Dihedral  :  6.727  86.999   1280
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.35 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.25), residues: 1122
  helix:  0.49 (0.20), residues: 680
  sheet:  0.61 (1.20), residues: 24
  loop : -1.50 (0.28), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 408 
 HIS   0.008   0.001   HIS A 490 
 PHE   0.027   0.001   PHE B 309 
 TYR   0.015   0.001   TYR A 559 
 ARG   0.002   0.000   ARG B 457 

*********************** 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
  114 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 1.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 MET cc_start: 0.4590 (ttt) cc_final: 0.3606 (tpt)
REVERT: A  409 MET cc_start: 0.9213 (tmm) cc_final: 0.8738 (ppp)
REVERT: A  607 MET cc_start: 0.7911 (tmm) cc_final: 0.7609 (tmm)
REVERT: B  229 LEU cc_start: 0.9716 (mm) cc_final: 0.9462 (pp)
REVERT: B  269 PHE cc_start: 0.9726 (t80) cc_final: 0.9477 (t80)
REVERT: B  310 MET cc_start: 0.5984 (ptp) cc_final: 0.5594 (ptm)
REVERT: B  357 ILE cc_start: 0.9793 (mm) cc_final: 0.9527 (tp)
REVERT: B  367 TYR cc_start: 0.9305 (t80) cc_final: 0.8690 (t80)
REVERT: B  409 MET cc_start: 0.8579 (ppp) cc_final: 0.8372 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1699
  time to fit residues: 29.7407
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  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 104 optimal weight:    0.3980
   chunk 14 optimal weight:    8.9990
   chunk 98 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 105 optimal weight:   20.0000
   chunk 84 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   chunk 101 optimal weight:    6.9990
   chunk 87 optimal weight:    7.9990
   overall best weight:    3.0786

-------------------------------------------------------------------------------
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 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 571 ASN
** B 647 GLN ** 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 = 0.3300 r_free = 0.3300 target = 0.055535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.044411 restraints weight = 70347.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.045601 restraints weight = 51850.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.046489 restraints weight = 40932.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.3888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9050  Z= 0.182
  Angle     :  0.694  10.053  12278  Z= 0.358
  Chirality :  0.043   0.197   1498
  Planarity :  0.004   0.037   1522
  Dihedral  :  6.726  86.138   1280
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.79 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.25), residues: 1122
  helix:  0.54 (0.20), residues: 678
  sheet:  0.68 (1.20), residues: 24
  loop : -1.44 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 408 
 HIS   0.009   0.001   HIS A 490 
 PHE   0.025   0.001   PHE B 309 
 TYR   0.016   0.001   TYR A 559 
 ARG   0.003   0.000   ARG B 260 

*********************** 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
  114 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 MET cc_start: 0.4581 (ttt) cc_final: 0.3839 (tpt)
REVERT: A  409 MET cc_start: 0.9231 (tmm) cc_final: 0.8737 (ppp)
REVERT: A  607 MET cc_start: 0.7859 (tmm) cc_final: 0.7551 (tmm)
REVERT: B  229 LEU cc_start: 0.9730 (mm) cc_final: 0.9478 (pp)
REVERT: B  269 PHE cc_start: 0.9742 (t80) cc_final: 0.9503 (t80)
REVERT: B  308 PHE cc_start: 0.9172 (t80) cc_final: 0.8918 (t80)
REVERT: B  310 MET cc_start: 0.5250 (ptp) cc_final: 0.4907 (ptm)
REVERT: B  357 ILE cc_start: 0.9790 (mm) cc_final: 0.9522 (tp)
REVERT: B  367 TYR cc_start: 0.9283 (t80) cc_final: 0.8971 (t80)
REVERT: B  384 TYR cc_start: 0.9322 (t80) cc_final: 0.8809 (t80)
REVERT: B  409 MET cc_start: 0.8577 (ppp) cc_final: 0.8366 (ppp)
REVERT: B  484 MET cc_start: 0.8980 (tpt) cc_final: 0.8353 (tpp)
REVERT: B  530 MET cc_start: 0.9157 (mpp) cc_final: 0.8910 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1606
  time to fit residues: 27.8812
Evaluate side-chains
  93 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 75 optimal weight:    0.0970
   chunk 28 optimal weight:    5.9990
   chunk 59 optimal weight:   20.0000
   chunk 34 optimal weight:   20.0000
   chunk 35 optimal weight:    8.9990
   chunk 4 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 111 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 33 optimal weight:    9.9990
   overall best weight:    2.3984

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

Flipped N/Q/H residues before XYZ refinement:
** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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**
** B 647 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 = 0.3316 r_free = 0.3316 target = 0.056044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.044985 restraints weight = 69207.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.046173 restraints weight = 51043.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.047065 restraints weight = 40257.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.4011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9050  Z= 0.163
  Angle     :  0.696  10.703  12278  Z= 0.353
  Chirality :  0.043   0.174   1498
  Planarity :  0.003   0.038   1522
  Dihedral  :  6.678  86.153   1280
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.08 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.25), residues: 1122
  helix:  0.54 (0.20), residues: 682
  sheet:  1.08 (1.13), residues: 26
  loop : -1.43 (0.28), residues: 414

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

*********************** 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
  113 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 GLU cc_start: 0.9420 (mp0) cc_final: 0.9068 (pm20)
REVERT: A  308 PHE cc_start: 0.9183 (t80) cc_final: 0.8829 (t80)
REVERT: A  310 MET cc_start: 0.4504 (ttt) cc_final: 0.3465 (ptm)
REVERT: A  607 MET cc_start: 0.7866 (tmm) cc_final: 0.7548 (tmm)
REVERT: B  196 TYR cc_start: 0.8478 (m-80) cc_final: 0.8129 (m-80)
REVERT: B  229 LEU cc_start: 0.9727 (mm) cc_final: 0.9458 (pp)
REVERT: B  269 PHE cc_start: 0.9735 (t80) cc_final: 0.9503 (t80)
REVERT: B  308 PHE cc_start: 0.9125 (t80) cc_final: 0.8905 (t80)
REVERT: B  310 MET cc_start: 0.5237 (ptp) cc_final: 0.4912 (ptm)
REVERT: B  357 ILE cc_start: 0.9788 (mm) cc_final: 0.9524 (tp)
REVERT: B  367 TYR cc_start: 0.9248 (t80) cc_final: 0.8936 (t80)
REVERT: B  384 TYR cc_start: 0.9294 (t80) cc_final: 0.8807 (t80)
REVERT: B  484 MET cc_start: 0.8974 (tpt) cc_final: 0.8439 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1901
  time to fit residues: 33.2333
Evaluate side-chains
  93 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 68 optimal weight:    9.9990
   chunk 76 optimal weight:    8.9990
   chunk 24 optimal weight:    0.0470
   chunk 0 optimal weight:   20.0000
   chunk 18 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9990
   chunk 111 optimal weight:    6.9990
   overall best weight:    2.0084

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

Flipped N/Q/H residues before XYZ refinement:
** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.056513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.045377 restraints weight = 68693.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.046565 restraints weight = 50757.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.047470 restraints weight = 40094.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.4068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9050  Z= 0.155
  Angle     :  0.694   9.141  12278  Z= 0.349
  Chirality :  0.043   0.174   1498
  Planarity :  0.003   0.038   1522
  Dihedral  :  6.622  85.683   1280
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.26 %
    Favored  : 94.47 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.25), residues: 1122
  helix:  0.62 (0.20), residues: 670
  sheet:  0.06 (0.82), residues: 46
  loop : -1.36 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 408 
 HIS   0.007   0.001   HIS A 490 
 PHE   0.029   0.001   PHE B 309 
 TYR   0.017   0.001   TYR A 559 
 ARG   0.002   0.000   ARG A 557 

********************** 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
  111 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 GLU cc_start: 0.9416 (mp0) cc_final: 0.9043 (mp0)
REVERT: A  308 PHE cc_start: 0.9185 (t80) cc_final: 0.8868 (t80)
REVERT: A  310 MET cc_start: 0.4483 (ttt) cc_final: 0.3436 (ptm)
REVERT: A  607 MET cc_start: 0.7863 (tmm) cc_final: 0.7542 (tmm)
REVERT: B  196 TYR cc_start: 0.8454 (m-80) cc_final: 0.8062 (m-80)
REVERT: B  269 PHE cc_start: 0.9737 (t80) cc_final: 0.9507 (t80)
REVERT: B  308 PHE cc_start: 0.9114 (t80) cc_final: 0.8900 (t80)
REVERT: B  310 MET cc_start: 0.5118 (ptp) cc_final: 0.4843 (ptm)
REVERT: B  357 ILE cc_start: 0.9781 (mm) cc_final: 0.9508 (tp)
REVERT: B  367 TYR cc_start: 0.9242 (t80) cc_final: 0.8917 (t80)
REVERT: B  384 TYR cc_start: 0.9312 (t80) cc_final: 0.8857 (t80)
REVERT: B  484 MET cc_start: 0.8919 (tpt) cc_final: 0.8341 (tpp)
REVERT: B  530 MET cc_start: 0.9181 (mpp) cc_final: 0.8893 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1623
  time to fit residues: 27.3855
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  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 57 optimal weight:    9.9990
   chunk 64 optimal weight:    6.9990
   chunk 41 optimal weight:   10.0000
   chunk 65 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 53 optimal weight:   20.0000
   chunk 82 optimal weight:    3.9990
   chunk 91 optimal weight:    0.0970
   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 164 GLN
** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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**
** B 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.055155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.044426 restraints weight = 70706.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.045552 restraints weight = 52445.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.046429 restraints weight = 41678.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.4340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9050  Z= 0.182
  Angle     :  0.709  10.949  12278  Z= 0.359
  Chirality :  0.043   0.174   1498
  Planarity :  0.004   0.040   1522
  Dihedral  :  6.767  86.064   1280
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.44 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.25), residues: 1122
  helix:  0.63 (0.20), residues: 668
  sheet:  1.05 (1.11), residues: 26
  loop : -1.41 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 408 
 HIS   0.007   0.001   HIS A 490 
 PHE   0.029   0.002   PHE B 309 
 TYR   0.016   0.001   TYR A 559 
 ARG   0.004   0.000   ARG A 557 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2564.26 seconds
wall clock time: 46 minutes 29.04 seconds (2789.04 seconds total)