Starting phenix.real_space_refine
on Fri Aug 22 22:57:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k0x_36780/08_2025/8k0x_36780.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k0x_36780/08_2025/8k0x_36780.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k0x_36780/08_2025/8k0x_36780.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k0x_36780/08_2025/8k0x_36780.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k0x_36780/08_2025/8k0x_36780.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k0x_36780/08_2025/8k0x_36780.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.134
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: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    5507      2.51       5
     N    1408      2.21       5
     O    1480      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8447
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 542, 4214
          Classifications: {'peptide': 542}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 523}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Unusual residues: {'A8S': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C
  Time building chain proxies: 2.78, per 1000 atoms: 0.33
  Number of scatterers: 8447
  At special positions: 0
  Unit cell: (86.9, 100.1, 121, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1480      8.00
     N    1408      7.00
     C    5507      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.58
  Conformation dependent library (CDL) restraints added in 413.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1988

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 6 sheets defined
      55.2% alpha, 4.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 106 through 113
      removed outlier: 3.575A  pdb=" N   LEU A 110 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU A 111 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ASN A 112 " --> pdb=" O   SER A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 140
      removed outlier: 3.654A  pdb=" N   LEU A 139 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LYS A 140 " --> pdb=" O   GLN A 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 136 through 140'
    Processing helix  chain 'A' and resid 156 through 169
      removed outlier: 3.758A  pdb=" N   LEU A 167 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A 169 " --> pdb=" O   ALA A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 189
    Processing helix  chain 'A' and resid 208 through 219
      removed outlier: 3.715A  pdb=" N   LYS A 213 " --> pdb=" O   GLY A 209 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ARG A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA A 218 " --> pdb=" O   ARG A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 256
      removed outlier: 3.563A  pdb=" N   ARG A 244 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 273
      removed outlier: 3.533A  pdb=" N   GLN A 273 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 303
      removed outlier: 3.939A  pdb=" N   SER A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL A 302 " --> pdb=" O   TYR A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 319
      removed outlier: 3.629A  pdb=" N   LEU A 316 " --> pdb=" O   PRO A 312 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 349
      removed outlier: 3.614A  pdb=" N   THR A 343 " --> pdb=" O   GLN A 339 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ASP A 346 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   THR A 347 " --> pdb=" O   THR A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 354
      removed outlier: 4.013A  pdb=" N   VAL A 353 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LYS A 354 " --> pdb=" O   ALA A 350 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 349 through 354'
    Processing helix  chain 'A' and resid 380 through 397
      removed outlier: 3.744A  pdb=" N   ALA A 384 " --> pdb=" O   THR A 380 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   TRP A 386 " --> pdb=" O   CYS A 382 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLN A 389 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE A 392 " --> pdb=" O   SER A 388 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU A 393 " --> pdb=" O   GLN A 389 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   HIS A 395 " --> pdb=" O   CYS A 391 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A 397 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 406
    Processing helix  chain 'A' and resid 407 through 425
      removed outlier: 3.813A  pdb=" N   PHE A 412 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLN A 413 " --> pdb=" O   LEU A 409 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   VAL A 414 " --> pdb=" O   ARG A 410 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   LEU A 420 " --> pdb=" O   ALA A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 454
      removed outlier: 3.723A  pdb=" N   ARG A 436 " --> pdb=" O   ASP A 432 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLY A 438 " --> pdb=" O   HIS A 434 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   SER A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLY A 448 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
      removed outlier: 3.563A  pdb=" N   ASN A 454 " --> pdb=" O   LEU A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 461
      No H-bonds generated for 'chain 'A' and resid 459 through 461'
    Processing helix  chain 'A' and resid 462 through 471
      removed outlier: 3.576A  pdb=" N   THR A 467 " --> pdb=" O   ARG A 463 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ARG A 468 " --> pdb=" O   ALA A 464 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ALA A 471 " --> pdb=" O   THR A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 489
      removed outlier: 3.654A  pdb=" N   TYR A 480 " --> pdb=" O   THR A 476 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ALA A 483 " --> pdb=" O   SER A 479 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   HIS A 484 " --> pdb=" O   TYR A 480 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU A 486 " --> pdb=" O   MET A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 505
      removed outlier: 3.812A  pdb=" N   THR A 501 " --> pdb=" O   ALA A 497 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   PHE A 502 " --> pdb=" O   SER A 498 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   TRP A 505 " --> pdb=" O   THR A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 542
      removed outlier: 3.550A  pdb=" N   THR A 519 " --> pdb=" O   PRO A 515 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLY A 532 " --> pdb=" O   LEU A 528 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   LEU A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLY A 534 " --> pdb=" O   SER A 530 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   MET A 542 " --> pdb=" O   GLY A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 561
      removed outlier: 3.520A  pdb=" N   VAL A 553 " --> pdb=" O   THR A 549 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL A 559 " --> pdb=" O   MET A 555 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   THR A 561 " --> pdb=" O   ALA A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 579
      removed outlier: 3.782A  pdb=" N   LYS A 577 " --> pdb=" O   VAL A 574 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   VAL A 579 " --> pdb=" O   MET A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 594
      removed outlier: 3.866A  pdb=" N   TYR A 584 " --> pdb=" O   SER A 580 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU A 588 " --> pdb=" O   TYR A 584 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA A 591 " --> pdb=" O   ARG A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 655
      removed outlier: 3.782A  pdb=" N   LEU A 642 " --> pdb=" O   SER A 638 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU A 644 " --> pdb=" O   GLY A 640 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TYR A 649 " --> pdb=" O   MET A 645 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ARG A 650 " --> pdb=" O   PHE A 646 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU A 652 " --> pdb=" O   GLY A 648 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 113
      removed outlier: 3.574A  pdb=" N   LEU C 110 " --> pdb=" O   GLY C 106 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU C 111 " --> pdb=" O   LYS C 107 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ASN C 112 " --> pdb=" O   SER C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 140
      removed outlier: 3.654A  pdb=" N   LEU C 139 " --> pdb=" O   LYS C 136 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LYS C 140 " --> pdb=" O   GLN C 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 136 through 140'
    Processing helix  chain 'C' and resid 156 through 169
      removed outlier: 3.758A  pdb=" N   LEU C 167 " --> pdb=" O   PHE C 163 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU C 169 " --> pdb=" O   ALA C 165 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 189
    Processing helix  chain 'C' and resid 208 through 219
      removed outlier: 3.716A  pdb=" N   LYS C 213 " --> pdb=" O   GLY C 209 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ARG C 214 " --> pdb=" O   GLY C 210 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ALA C 218 " --> pdb=" O   ARG C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 240 through 256
      removed outlier: 3.563A  pdb=" N   ARG C 244 " --> pdb=" O   THR C 240 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL C 246 " --> pdb=" O   ALA C 242 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA C 253 " --> pdb=" O   LEU C 249 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 268 through 273
      removed outlier: 3.532A  pdb=" N   GLN C 273 " --> pdb=" O   SER C 269 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 303
      removed outlier: 3.939A  pdb=" N   SER C 301 " --> pdb=" O   ALA C 297 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL C 302 " --> pdb=" O   TYR C 298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 311 through 319
      removed outlier: 3.628A  pdb=" N   LEU C 316 " --> pdb=" O   PRO C 312 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LEU C 317 " --> pdb=" O   ALA C 313 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 339 through 349
      removed outlier: 3.614A  pdb=" N   THR C 343 " --> pdb=" O   GLN C 339 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASP C 346 " --> pdb=" O   VAL C 342 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   THR C 347 " --> pdb=" O   THR C 343 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 349 through 354
      removed outlier: 4.012A  pdb=" N   VAL C 353 " --> pdb=" O   LEU C 349 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LYS C 354 " --> pdb=" O   ALA C 350 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 349 through 354'
    Processing helix  chain 'C' and resid 380 through 397
      removed outlier: 3.745A  pdb=" N   ALA C 384 " --> pdb=" O   THR C 380 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   TRP C 386 " --> pdb=" O   CYS C 382 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLN C 389 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ILE C 392 " --> pdb=" O   SER C 388 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU C 393 " --> pdb=" O   GLN C 389 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   HIS C 395 " --> pdb=" O   CYS C 391 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU C 397 " --> pdb=" O   LEU C 393 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 397 through 406
    Processing helix  chain 'C' and resid 407 through 425
      removed outlier: 3.814A  pdb=" N   PHE C 412 " --> pdb=" O   LEU C 408 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLN C 413 " --> pdb=" O   LEU C 409 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   VAL C 414 " --> pdb=" O   ARG C 410 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LEU C 420 " --> pdb=" O   ALA C 416 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 432 through 454
      removed outlier: 3.723A  pdb=" N   ARG C 436 " --> pdb=" O   ASP C 432 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLY C 438 " --> pdb=" O   HIS C 434 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   SER C 444 " --> pdb=" O   LEU C 440 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   GLY C 448 " --> pdb=" O   SER C 444 " (cutoff:3.500A)
      Proline residue:  C 451  - end of helix
      removed outlier: 3.563A  pdb=" N   ASN C 454 " --> pdb=" O   LEU C 450 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 459 through 461
      No H-bonds generated for 'chain 'C' and resid 459 through 461'
    Processing helix  chain 'C' and resid 462 through 471
      removed outlier: 3.576A  pdb=" N   THR C 467 " --> pdb=" O   ARG C 463 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ARG C 468 " --> pdb=" O   ALA C 464 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ALA C 471 " --> pdb=" O   THR C 467 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 476 through 489
      removed outlier: 3.654A  pdb=" N   TYR C 480 " --> pdb=" O   THR C 476 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ALA C 483 " --> pdb=" O   SER C 479 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   HIS C 484 " --> pdb=" O   TYR C 480 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU C 486 " --> pdb=" O   MET C 482 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 494 through 505
      removed outlier: 3.813A  pdb=" N   THR C 501 " --> pdb=" O   ALA C 497 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   PHE C 502 " --> pdb=" O   SER C 498 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   TRP C 505 " --> pdb=" O   THR C 501 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 513 through 542
      removed outlier: 3.550A  pdb=" N   THR C 519 " --> pdb=" O   PRO C 515 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY C 532 " --> pdb=" O   LEU C 528 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   LEU C 533 " --> pdb=" O   ALA C 529 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLY C 534 " --> pdb=" O   SER C 530 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   MET C 542 " --> pdb=" O   GLY C 538 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 549 through 561
      removed outlier: 3.521A  pdb=" N   VAL C 553 " --> pdb=" O   THR C 549 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL C 559 " --> pdb=" O   MET C 555 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   THR C 561 " --> pdb=" O   ALA C 557 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 573 through 579
      removed outlier: 3.783A  pdb=" N   LYS C 577 " --> pdb=" O   VAL C 574 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   VAL C 579 " --> pdb=" O   MET C 576 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 580 through 594
      removed outlier: 3.867A  pdb=" N   TYR C 584 " --> pdb=" O   SER C 580 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU C 588 " --> pdb=" O   TYR C 584 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ALA C 591 " --> pdb=" O   ARG C 587 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 636 through 655
      removed outlier: 3.782A  pdb=" N   LEU C 642 " --> pdb=" O   SER C 638 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU C 644 " --> pdb=" O   GLY C 640 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TYR C 649 " --> pdb=" O   MET C 645 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ARG C 650 " --> pdb=" O   PHE C 646 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU C 652 " --> pdb=" O   GLY C 648 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91
    Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 262
      removed outlier: 6.462A  pdb=" N   MET A  97 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU A 281 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLY A 290 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   PHE A 288 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145
      removed outlier: 6.155A  pdb=" N   GLY A 143 " --> pdb=" O   VAL A 229 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 89 through 91
    Processing sheet with id=AA5, first strand: chain 'C' and resid 261 through 262
      removed outlier: 6.461A  pdb=" N   MET C  97 " --> pdb=" O   THR C 262 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU C 281 " --> pdb=" O   LEU C 100 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   GLY C 290 " --> pdb=" O   VAL C 278 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   PHE C 288 " --> pdb=" O   LEU C 280 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 142 through 145
      removed outlier: 6.154A  pdb=" N   GLY C 143 " --> pdb=" O   VAL C 229 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    294 hydrogen bonds defined for protein.
    852 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: 0.92

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2583
        1.34 -     1.45: 1523
        1.45 -     1.57: 4433
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 8623
  Sorted by residual:
  bond pdb=" C   ALA C 350 "
       pdb=" N   PRO C 351 "
    ideal  model  delta    sigma   weight residual
    1.339  1.405 -0.066 3.40e-02 8.65e+02 3.79e+00
  bond pdb=" C   ALA A 350 "
       pdb=" N   PRO A 351 "
    ideal  model  delta    sigma   weight residual
    1.339  1.405 -0.066 3.40e-02 8.65e+02 3.72e+00
  bond pdb=" C7  A8S C 701 "
       pdb=" C8  A8S C 701 "
    ideal  model  delta    sigma   weight residual
    1.534  1.500  0.034 2.00e-02 2.50e+03 2.81e+00
  bond pdb=" CG  LEU A 509 "
       pdb=" CD2 LEU A 509 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.050 3.30e-02 9.18e+02 2.28e+00
  bond pdb=" CG  LEU C 509 "
       pdb=" CD2 LEU C 509 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.050 3.30e-02 9.18e+02 2.27e+00
  ... (remaining 8618 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 11229
        2.31 -     4.61: 380
        4.61 -     6.92: 63
        6.92 -     9.23: 19
        9.23 -    11.53: 2
  Bond angle restraints: 11693
  Sorted by residual:
  angle pdb=" N   PHE A 203 "
        pdb=" CA  PHE A 203 "
        pdb=" C   PHE A 203 "
      ideal   model   delta    sigma   weight residual
     114.62  107.72    6.90 1.14e+00 7.69e-01 3.67e+01
  angle pdb=" N   PHE C 203 "
        pdb=" CA  PHE C 203 "
        pdb=" C   PHE C 203 "
      ideal   model   delta    sigma   weight residual
     114.62  107.76    6.86 1.14e+00 7.69e-01 3.62e+01
  angle pdb=" CA  VAL C 514 "
        pdb=" C   VAL C 514 "
        pdb=" N   PRO C 515 "
      ideal   model   delta    sigma   weight residual
     118.88  124.60   -5.72 1.54e+00 4.22e-01 1.38e+01
  angle pdb=" CA  VAL A 514 "
        pdb=" C   VAL A 514 "
        pdb=" N   PRO A 515 "
      ideal   model   delta    sigma   weight residual
     118.88  124.56   -5.68 1.54e+00 4.22e-01 1.36e+01
  angle pdb=" CA  PHE C 203 "
        pdb=" C   PHE C 203 "
        pdb=" N   ILE C 204 "
      ideal   model   delta    sigma   weight residual
     119.71  115.40    4.31 1.17e+00 7.31e-01 1.35e+01
  ... (remaining 11688 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.07: 4779
       15.07 -    30.13: 235
       30.13 -    45.20: 58
       45.20 -    60.27: 2
       60.27 -    75.34: 4
  Dihedral angle restraints: 5078
    sinusoidal: 1980
      harmonic: 3098
  Sorted by residual:
  dihedral pdb=" CA  VAL C  45 "
           pdb=" C   VAL C  45 "
           pdb=" N   CYS C  46 "
           pdb=" CA  CYS C  46 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.32  -22.68     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" CA  VAL A  45 "
           pdb=" C   VAL A  45 "
           pdb=" N   CYS A  46 "
           pdb=" CA  CYS A  46 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.40  -22.60     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  PRO A 570 "
           pdb=" C   PRO A 570 "
           pdb=" N   SER A 571 "
           pdb=" CA  SER A 571 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.70   20.30     0      5.00e+00 4.00e-02 1.65e+01
  ... (remaining 5075 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 992
       0.058 -    0.115: 323
       0.115 -    0.173: 59
       0.173 -    0.231: 9
       0.231 -    0.289: 8
  Chirality restraints: 1391
  Sorted by residual:
  chirality pdb=" CB  VAL A  43 "
            pdb=" CA  VAL A  43 "
            pdb=" CG1 VAL A  43 "
            pdb=" CG2 VAL A  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" CB  VAL C  43 "
            pdb=" CA  VAL C  43 "
            pdb=" CG1 VAL C  43 "
            pdb=" CG2 VAL C  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CB  VAL A 514 "
            pdb=" CA  VAL A 514 "
            pdb=" CG1 VAL A 514 "
            pdb=" CG2 VAL A 514 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.72e+00
  ... (remaining 1388 not shown)

  Planarity restraints: 1434
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 459 "   -0.035 5.00e-02 4.00e+02   5.19e-02 4.31e+00
        pdb=" N   PRO A 460 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 460 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 460 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 459 "    0.035 5.00e-02 4.00e+02   5.19e-02 4.31e+00
        pdb=" N   PRO C 460 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO C 460 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C 460 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 311 "   -0.031 5.00e-02 4.00e+02   4.65e-02 3.46e+00
        pdb=" N   PRO A 312 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 312 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 312 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1431 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2585
        2.83 -     3.34: 7052
        3.34 -     3.86: 12265
        3.86 -     4.38: 14638
        4.38 -     4.90: 26229
  Nonbonded interactions: 62769
  Sorted by model distance:
  nonbonded pdb=" O   SER A 282 "
            pdb=" OG  SER A 282 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   SER C 282 "
            pdb=" OG  SER C 282 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" OE1 GLU C 462 "
            pdb=" OH  TYR C 480 "
     model   vdw
     2.434 3.040
  nonbonded pdb=" OE1 GLU A 462 "
            pdb=" OH  TYR A 480 "
     model   vdw
     2.434 3.040
  nonbonded pdb=" OE2 GLU A  95 "
            pdb=" OG1 THR A 277 "
     model   vdw
     2.467 3.040
  ... (remaining 62764 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'C' and resid 35 through 662)
}

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 individual isotropic
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:             0.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.550
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
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      :  0.008   0.069   8623  Z= 0.327
  Angle     :  1.045  11.533  11693  Z= 0.556
  Chirality :  0.059   0.289   1391
  Planarity :  0.007   0.052   1434
  Dihedral  :  9.778  75.335   3090
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 1.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -6.65 (0.16), residues: 1064
  helix: -4.74 (0.08), residues: 584
  sheet: -3.87 (0.47), residues: 84
  loop : -3.63 (0.25), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 214 
 TYR   0.024   0.003   TYR A 508 
 PHE   0.032   0.004   PHE C  96 
 TRP   0.022   0.003   TRP C 386 
 HIS   0.012   0.003   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00783 ( 8623)
  covalent geometry    : angle       1.04462 (11693)
  hydrogen bonds       : bond        0.35020 (  294)
  hydrogen bonds       : angle      10.78841 (  852)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  289 VAL cc_start: 0.8586 (t) cc_final: 0.8356 (m)
REVERT: A  314 ASP cc_start: 0.8014 (t0) cc_final: 0.7654 (m-30)
REVERT: C  289 VAL cc_start: 0.8571 (t) cc_final: 0.8337 (m)
REVERT: C  314 ASP cc_start: 0.7915 (t0) cc_final: 0.7660 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1325
  time to fit residues: 28.9080
Evaluate side-chains
  106 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.4980
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 247 GLN
A 461 GLN
A 531 GLN
C 461 GLN
C 531 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.160668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.125430 restraints weight = 9902.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 1.74
r_work: 0.3081 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.2305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8623  Z= 0.116
  Angle     :  0.596   6.849  11693  Z= 0.310
  Chirality :  0.041   0.144   1391
  Planarity :  0.005   0.037   1434
  Dihedral  :  5.171  39.074   1196
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  6.64 %
    Favored  : 91.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.71 (0.20), residues: 1064
  helix: -3.04 (0.16), residues: 560
  sheet: -3.54 (0.51), residues: 82
  loop : -2.91 (0.26), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 117 
 TYR   0.011   0.001   TYR A 586 
 PHE   0.010   0.001   PHE A 583 
 TRP   0.009   0.002   TRP C 447 
 HIS   0.003   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8623)
  covalent geometry    : angle       0.59591 (11693)
  hydrogen bonds       : bond        0.04887 (  294)
  hydrogen bonds       : angle       4.78004 (  852)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A   90 MET cc_start: 0.8758 (ptm) cc_final: 0.8447 (ptt)
REVERT: A  314 ASP cc_start: 0.8225 (t0) cc_final: 0.7660 (m-30)
REVERT: A  318 ASP cc_start: 0.7394 (m-30) cc_final: 0.7183 (m-30)
REVERT: A  491 MET cc_start: 0.8567 (mmp) cc_final: 0.8174 (mmt)
REVERT: C   90 MET cc_start: 0.8775 (ptm) cc_final: 0.8470 (ptt)
REVERT: C  314 ASP cc_start: 0.8223 (t0) cc_final: 0.7667 (m-30)
REVERT: C  491 MET cc_start: 0.8585 (mmp) cc_final: 0.8171 (mmt)
  outliers start: 16
  outliers final: 12
  residues processed: 130
  average time/residue: 0.1343
  time to fit residues: 22.6098
Evaluate side-chains
  114 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  197 THR
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  514 VAL
Chi-restraints excluded: chain C residue  569 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 70 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0980
   chunk 105 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.156189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.120334 restraints weight = 9891.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 1.76
r_work: 0.3022 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8623  Z= 0.117
  Angle     :  0.564   6.873  11693  Z= 0.291
  Chirality :  0.041   0.151   1391
  Planarity :  0.004   0.035   1434
  Dihedral  :  4.753  37.127   1196
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  :  6.97 %
    Favored  : 90.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.54 (0.23), residues: 1064
  helix: -1.85 (0.20), residues: 550
  sheet: -3.41 (0.51), residues: 82
  loop : -2.63 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 158 
 TYR   0.012   0.001   TYR A 586 
 PHE   0.028   0.001   PHE A 502 
 TRP   0.010   0.001   TRP C 426 
 HIS   0.005   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8623)
  covalent geometry    : angle       0.56401 (11693)
  hydrogen bonds       : bond        0.04613 (  294)
  hydrogen bonds       : angle       4.17326 (  852)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A   90 MET cc_start: 0.8738 (ptm) cc_final: 0.8410 (ptt)
REVERT: A  314 ASP cc_start: 0.8241 (t0) cc_final: 0.7681 (m-30)
REVERT: A  531 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8800 (tt0)
REVERT: C   90 MET cc_start: 0.8807 (ptm) cc_final: 0.8472 (ptt)
REVERT: C  314 ASP cc_start: 0.8275 (t0) cc_final: 0.7636 (m-30)
REVERT: C  531 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8806 (tt0)
  outliers start: 23
  outliers final: 19
  residues processed: 122
  average time/residue: 0.1349
  time to fit residues: 21.2586
Evaluate side-chains
  115 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  531 GLN
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain C residue   85 SER
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  197 THR
Chi-restraints excluded: chain C residue  235 SER
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  514 VAL
Chi-restraints excluded: chain C residue  531 GLN
Chi-restraints excluded: chain C residue  569 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 106 optimal weight:    0.0270
   chunk 16 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0980
   chunk 60 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0270
   chunk 87 optimal weight:    4.9990
   chunk 66 optimal weight:    0.5980
   chunk 5 optimal weight:   10.0000
   overall best weight:    0.3498

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.157237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.120701 restraints weight = 10103.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 1.90
r_work: 0.3025 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2890 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   8623  Z= 0.086
  Angle     :  0.496   6.598  11693  Z= 0.255
  Chirality :  0.039   0.136   1391
  Planarity :  0.003   0.034   1434
  Dihedral  :  4.353  35.144   1196
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  :  7.52 %
    Favored  : 89.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.69 (0.25), residues: 1064
  helix: -0.98 (0.22), residues: 542
  sheet: -3.26 (0.52), residues: 82
  loop : -2.44 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 158 
 TYR   0.007   0.001   TYR C  47 
 PHE   0.026   0.001   PHE A 502 
 TRP   0.007   0.001   TRP A 426 
 HIS   0.003   0.000   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 ( 8623)
  covalent geometry    : angle       0.49605 (11693)
  hydrogen bonds       : bond        0.03327 (  294)
  hydrogen bonds       : angle       3.74755 (  852)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8770 (ptm) cc_final: 0.8462 (ptt)
REVERT: A  314 ASP cc_start: 0.8312 (t0) cc_final: 0.7710 (m-30)
REVERT: A  431 ARG cc_start: 0.8347 (ptp-110) cc_final: 0.8088 (ptp-110)
REVERT: A  531 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8822 (tt0)
REVERT: C   90 MET cc_start: 0.8811 (ptm) cc_final: 0.8506 (ptt)
REVERT: C  314 ASP cc_start: 0.8308 (t0) cc_final: 0.7669 (m-30)
REVERT: C  431 ARG cc_start: 0.8321 (ptp-110) cc_final: 0.8118 (ptp-110)
REVERT: C  531 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8830 (tt0)
  outliers start: 25
  outliers final: 19
  residues processed: 124
  average time/residue: 0.1312
  time to fit residues: 21.1573
Evaluate side-chains
  116 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  531 GLN
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  235 SER
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  514 VAL
Chi-restraints excluded: chain C residue  531 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0060
   chunk 26 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 71 optimal weight:    0.3980
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.6798

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.156906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.121435 restraints weight = 10002.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.76
r_work: 0.3038 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8623  Z= 0.102
  Angle     :  0.511   6.550  11693  Z= 0.262
  Chirality :  0.040   0.145   1391
  Planarity :  0.003   0.033   1434
  Dihedral  :  4.336  36.157   1196
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  :  8.06 %
    Favored  : 88.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.40 (0.25), residues: 1064
  helix: -0.70 (0.22), residues: 544
  sheet: -3.51 (0.45), residues: 94
  loop : -2.21 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 158 
 TYR   0.010   0.001   TYR A 586 
 PHE   0.020   0.001   PHE C 502 
 TRP   0.008   0.001   TRP C 426 
 HIS   0.005   0.001   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 8623)
  covalent geometry    : angle       0.51054 (11693)
  hydrogen bonds       : bond        0.03808 (  294)
  hydrogen bonds       : angle       3.71792 (  852)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8813 (ptm) cc_final: 0.8503 (ptt)
REVERT: A  314 ASP cc_start: 0.8341 (t0) cc_final: 0.7790 (m-30)
REVERT: A  531 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8813 (tt0)
REVERT: C   90 MET cc_start: 0.8861 (ptm) cc_final: 0.8564 (ptt)
REVERT: C  314 ASP cc_start: 0.8348 (t0) cc_final: 0.7795 (m-30)
REVERT: C  431 ARG cc_start: 0.8422 (ptp-110) cc_final: 0.8119 (mtm-85)
REVERT: C  531 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8823 (tt0)
  outliers start: 30
  outliers final: 23
  residues processed: 124
  average time/residue: 0.1272
  time to fit residues: 20.4029
Evaluate side-chains
  124 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  531 GLN
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain C residue   85 SER
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  187 SER
Chi-restraints excluded: chain C residue  223 ILE
Chi-restraints excluded: chain C residue  235 SER
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  514 VAL
Chi-restraints excluded: chain C residue  531 GLN
Chi-restraints excluded: chain C residue  569 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:    0.0470
   chunk 17 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 90 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0670
   chunk 21 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 81 optimal weight:    0.0770
   chunk 77 optimal weight:    4.9990
   overall best weight:    0.6376

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.145338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.107931 restraints weight = 9975.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.79
r_work: 0.3001 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8623  Z= 0.099
  Angle     :  0.500   6.533  11693  Z= 0.257
  Chirality :  0.040   0.130   1391
  Planarity :  0.003   0.034   1434
  Dihedral  :  4.273  35.654   1196
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  :  9.48 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.12 (0.25), residues: 1064
  helix: -0.46 (0.22), residues: 548
  sheet: -3.06 (0.46), residues: 96
  loop : -2.19 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 158 
 TYR   0.009   0.001   TYR C 586 
 PHE   0.022   0.001   PHE A 502 
 TRP   0.009   0.001   TRP C 426 
 HIS   0.005   0.001   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 8623)
  covalent geometry    : angle       0.50021 (11693)
  hydrogen bonds       : bond        0.03625 (  294)
  hydrogen bonds       : angle       3.66152 (  852)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 104
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8808 (ptm) cc_final: 0.8521 (ptt)
REVERT: A  179 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7254 (mp)
REVERT: A  285 LYS cc_start: 0.8699 (mppt) cc_final: 0.8437 (mppt)
REVERT: A  314 ASP cc_start: 0.8385 (t0) cc_final: 0.7902 (m-30)
REVERT: A  431 ARG cc_start: 0.8393 (ptp-110) cc_final: 0.8126 (mtt90)
REVERT: A  531 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8825 (tt0)
REVERT: C   90 MET cc_start: 0.8877 (ptm) cc_final: 0.8602 (ptt)
REVERT: C  314 ASP cc_start: 0.8385 (t0) cc_final: 0.7878 (m-30)
REVERT: C  531 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8836 (tt0)
  outliers start: 32
  outliers final: 27
  residues processed: 128
  average time/residue: 0.1102
  time to fit residues: 18.6023
Evaluate side-chains
  128 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 98
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  531 GLN
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain C residue   38 ILE
Chi-restraints excluded: chain C residue   85 SER
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  235 SER
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  514 VAL
Chi-restraints excluded: chain C residue  531 GLN
Chi-restraints excluded: chain C residue  569 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 27 optimal weight:    8.9990
   chunk 67 optimal weight:    0.5980
   chunk 73 optimal weight:    4.9990
   chunk 101 optimal weight:    0.4980
   chunk 29 optimal weight:    0.1980
   chunk 26 optimal weight:    3.9990
   chunk 60 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.8584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.153348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.116738 restraints weight = 10069.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 1.79
r_work: 0.3001 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8623  Z= 0.115
  Angle     :  0.523   6.553  11693  Z= 0.267
  Chirality :  0.041   0.134   1391
  Planarity :  0.003   0.037   1434
  Dihedral  :  4.347  35.409   1196
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  :  8.93 %
    Favored  : 86.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.11 (0.25), residues: 1064
  helix: -0.44 (0.22), residues: 564
  sheet: -3.17 (0.47), residues: 94
  loop : -2.23 (0.28), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 431 
 TYR   0.011   0.001   TYR C 586 
 PHE   0.024   0.001   PHE C 502 
 TRP   0.010   0.001   TRP A 426 
 HIS   0.005   0.001   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8623)
  covalent geometry    : angle       0.52275 (11693)
  hydrogen bonds       : bond        0.04045 (  294)
  hydrogen bonds       : angle       3.71994 (  852)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 100
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A   90 MET cc_start: 0.8830 (ptm) cc_final: 0.8545 (ptt)
REVERT: A  179 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7359 (mp)
REVERT: A  314 ASP cc_start: 0.8349 (t0) cc_final: 0.7847 (m-30)
REVERT: A  431 ARG cc_start: 0.8530 (ptp-110) cc_final: 0.8288 (mtt90)
REVERT: A  531 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.9035 (tt0)
REVERT: C   90 MET cc_start: 0.8900 (ptm) cc_final: 0.8627 (ptt)
REVERT: C  179 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7266 (mp)
REVERT: C  314 ASP cc_start: 0.8364 (t0) cc_final: 0.7854 (m-30)
REVERT: C  531 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.9047 (tt0)
  outliers start: 40
  outliers final: 31
  residues processed: 131
  average time/residue: 0.1140
  time to fit residues: 19.9122
Evaluate side-chains
  130 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 95
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  531 GLN
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain C residue   38 ILE
Chi-restraints excluded: chain C residue   85 SER
Chi-restraints excluded: chain C residue   97 MET
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  187 SER
Chi-restraints excluded: chain C residue  197 THR
Chi-restraints excluded: chain C residue  235 SER
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  514 VAL
Chi-restraints excluded: chain C residue  531 GLN
Chi-restraints excluded: chain C residue  569 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 10 optimal weight:    0.0970
   chunk 85 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0030
   overall best weight:    0.9792

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.152468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.115872 restraints weight = 9944.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 1.77
r_work: 0.2971 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2836 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.3504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8623  Z= 0.124
  Angle     :  0.533   6.574  11693  Z= 0.272
  Chirality :  0.041   0.135   1391
  Planarity :  0.004   0.037   1434
  Dihedral  :  4.399  33.591   1196
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  :  9.26 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.98 (0.25), residues: 1064
  helix: -0.36 (0.22), residues: 562
  sheet: -2.99 (0.48), residues: 94
  loop : -2.15 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 431 
 TYR   0.010   0.001   TYR A 586 
 PHE   0.014   0.001   PHE C 304 
 TRP   0.011   0.001   TRP C 426 
 HIS   0.006   0.001   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8623)
  covalent geometry    : angle       0.53280 (11693)
  hydrogen bonds       : bond        0.04125 (  294)
  hydrogen bonds       : angle       3.73849 (  852)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 99
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A   90 MET cc_start: 0.8812 (ptm) cc_final: 0.8525 (ptt)
REVERT: A  179 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7412 (mp)
REVERT: A  314 ASP cc_start: 0.8356 (t0) cc_final: 0.7868 (m-30)
REVERT: A  431 ARG cc_start: 0.8562 (ptp-110) cc_final: 0.8348 (mtt90)
REVERT: A  531 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.9033 (tt0)
REVERT: C   90 MET cc_start: 0.8836 (ptm) cc_final: 0.8561 (ptt)
REVERT: C  179 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7349 (mp)
REVERT: C  314 ASP cc_start: 0.8384 (t0) cc_final: 0.7886 (m-30)
REVERT: C  531 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.9047 (tt0)
  outliers start: 39
  outliers final: 33
  residues processed: 128
  average time/residue: 0.1160
  time to fit residues: 19.6874
Evaluate side-chains
  134 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 97
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  531 GLN
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain C residue   38 ILE
Chi-restraints excluded: chain C residue   85 SER
Chi-restraints excluded: chain C residue   97 MET
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  187 SER
Chi-restraints excluded: chain C residue  197 THR
Chi-restraints excluded: chain C residue  223 ILE
Chi-restraints excluded: chain C residue  235 SER
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  514 VAL
Chi-restraints excluded: chain C residue  531 GLN
Chi-restraints excluded: chain C residue  569 VAL
Chi-restraints excluded: chain C residue  633 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 91 optimal weight:    0.4980
   chunk 102 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 80 optimal weight:    9.9990
   chunk 37 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9990
   chunk 94 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.7984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.153562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.117003 restraints weight = 9907.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 1.77
r_work: 0.2977 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.3592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8623  Z= 0.110
  Angle     :  0.512   6.639  11693  Z= 0.262
  Chirality :  0.041   0.132   1391
  Planarity :  0.003   0.036   1434
  Dihedral  :  4.280  33.624   1196
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  :  9.59 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.80 (0.25), residues: 1064
  helix: -0.19 (0.22), residues: 562
  sheet: -2.87 (0.49), residues: 94
  loop : -2.12 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 431 
 TYR   0.009   0.001   TYR C 586 
 PHE   0.012   0.001   PHE C 304 
 TRP   0.009   0.001   TRP C 426 
 HIS   0.005   0.001   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8623)
  covalent geometry    : angle       0.51236 (11693)
  hydrogen bonds       : bond        0.03819 (  294)
  hydrogen bonds       : angle       3.65333 (  852)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 100
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8808 (ptm) cc_final: 0.8516 (ptt)
REVERT: A  140 LYS cc_start: 0.7566 (mtmp) cc_final: 0.7307 (ptpp)
REVERT: A  179 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7441 (mp)
REVERT: A  314 ASP cc_start: 0.8420 (t0) cc_final: 0.7965 (m-30)
REVERT: A  431 ARG cc_start: 0.8580 (ptp-110) cc_final: 0.8371 (mtt90)
REVERT: C   90 MET cc_start: 0.8836 (ptm) cc_final: 0.8567 (ptt)
REVERT: C  179 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7398 (mp)
REVERT: C  314 ASP cc_start: 0.8439 (t0) cc_final: 0.7974 (m-30)
REVERT: C  474 MET cc_start: 0.9073 (mtp) cc_final: 0.8809 (mtp)
  outliers start: 38
  outliers final: 32
  residues processed: 127
  average time/residue: 0.1271
  time to fit residues: 21.2179
Evaluate side-chains
  130 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 96
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue   97 MET
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain C residue   85 SER
Chi-restraints excluded: chain C residue   97 MET
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  187 SER
Chi-restraints excluded: chain C residue  197 THR
Chi-restraints excluded: chain C residue  223 ILE
Chi-restraints excluded: chain C residue  235 SER
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  514 VAL
Chi-restraints excluded: chain C residue  569 VAL
Chi-restraints excluded: chain C residue  633 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 1 optimal weight:    0.1980
   chunk 86 optimal weight:    1.9990
   chunk 95 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 531 GLN
C 531 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.152986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.116255 restraints weight = 9898.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 1.78
r_work: 0.2999 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2864 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.3645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8623  Z= 0.113
  Angle     :  0.519   6.760  11693  Z= 0.266
  Chirality :  0.041   0.133   1391
  Planarity :  0.003   0.036   1434
  Dihedral  :  4.305  33.857   1196
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 10.24 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.70 (0.25), residues: 1064
  helix: -0.10 (0.22), residues: 562
  sheet: -2.78 (0.50), residues: 94
  loop : -2.09 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 431 
 TYR   0.009   0.001   TYR C 586 
 PHE   0.012   0.001   PHE C 304 
 TRP   0.010   0.001   TRP C 426 
 HIS   0.005   0.001   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8623)
  covalent geometry    : angle       0.51864 (11693)
  hydrogen bonds       : bond        0.03923 (  294)
  hydrogen bonds       : angle       3.65297 (  852)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 96
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A   90 MET cc_start: 0.8796 (ptm) cc_final: 0.8514 (ptt)
REVERT: A  126 LYS cc_start: 0.6937 (mmtt) cc_final: 0.6080 (tmtt)
REVERT: A  140 LYS cc_start: 0.7535 (mtmp) cc_final: 0.7275 (ptpp)
REVERT: A  179 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7421 (mp)
REVERT: A  314 ASP cc_start: 0.8367 (t0) cc_final: 0.7868 (m-30)
REVERT: A  431 ARG cc_start: 0.8564 (ptp-110) cc_final: 0.8341 (mtt90)
REVERT: C   90 MET cc_start: 0.8874 (ptm) cc_final: 0.8608 (ptt)
REVERT: C  179 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7383 (mp)
REVERT: C  314 ASP cc_start: 0.8383 (t0) cc_final: 0.7884 (m-30)
  outliers start: 33
  outliers final: 31
  residues processed: 119
  average time/residue: 0.1254
  time to fit residues: 19.5338
Evaluate side-chains
  129 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 96
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  235 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain C residue   85 SER
Chi-restraints excluded: chain C residue   97 MET
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  187 SER
Chi-restraints excluded: chain C residue  197 THR
Chi-restraints excluded: chain C residue  223 ILE
Chi-restraints excluded: chain C residue  235 SER
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  514 VAL
Chi-restraints excluded: chain C residue  569 VAL
Chi-restraints excluded: chain C residue  633 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    1.1582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.141618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.103979 restraints weight = 10009.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 1.76
r_work: 0.2950 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2815 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8623  Z= 0.139
  Angle     :  0.550   6.836  11693  Z= 0.280
  Chirality :  0.042   0.135   1391
  Planarity :  0.004   0.036   1434
  Dihedral  :  4.443  33.639   1196
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 10.24 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.76 (0.25), residues: 1064
  helix: -0.20 (0.22), residues: 564
  sheet: -2.70 (0.51), residues: 92
  loop : -2.08 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 431 
 TYR   0.011   0.001   TYR A 586 
 PHE   0.013   0.001   PHE C 304 
 TRP   0.011   0.001   TRP C 426 
 HIS   0.006   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 8623)
  covalent geometry    : angle       0.55014 (11693)
  hydrogen bonds       : bond        0.04332 (  294)
  hydrogen bonds       : angle       3.76748 (  852)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2363.53 seconds
wall clock time: 41 minutes 7.18 seconds (2467.18 seconds total)