Starting phenix.real_space_refine
on Wed Feb 12 23:00:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k0x_36780/02_2025/8k0x_36780.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k0x_36780/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k0x_36780/02_2025/8k0x_36780.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k0x_36780/02_2025/8k0x_36780.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k0x_36780/02_2025/8k0x_36780.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k0x_36780/02_2025/8k0x_36780.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 7.74, per 1000 atoms: 0.92
  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: 2.04
  Conformation dependent library (CDL) restraints added in 972.8 milliseconds
  

  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: 0.85
  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: 2.19

  Time building geometry restraints manager: 2.34 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:             0.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.750
  Find NCS groups from input model:        0.310
  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:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.320
-------------------------------------------------------------------------------
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= 0.505
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.022   0.003   TRP C 386 
 HIS   0.012   0.003   HIS A 427 
 PHE   0.032   0.004   PHE C  96 
 TYR   0.024   0.003   TYR A 508 
 ARG   0.007   0.001   ARG A 214 

*********************** 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  : 0.715 
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: 0.3347
  time to fit residues: 73.1085
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  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 81 optimal weight:    0.0980
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0370
   chunk 55 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.4658

-------------------------------------------------------------------------------
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 = 0.3816 r_free = 0.3816 target = 0.163784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.129139 restraints weight = 9705.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.71
r_work: 0.3073 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   8623  Z= 0.143
  Angle     :  0.583   6.802  11693  Z= 0.305
  Chirality :  0.041   0.143   1391
  Planarity :  0.005   0.036   1434
  Dihedral  :  5.171  39.624   1196
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  6.54 %
    Favored  : 91.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.72 (0.20), residues: 1064
  helix: -3.02 (0.16), residues: 562
  sheet: -3.56 (0.51), residues: 82
  loop : -2.95 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 447 
 HIS   0.003   0.001   HIS A 219 
 PHE   0.008   0.001   PHE A  96 
 TYR   0.010   0.001   TYR A 586 
 ARG   0.004   0.001   ARG C 117 

*********************** 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
  141 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.895 
Fit side-chains
REVERT: A   90 MET cc_start: 0.8766 (ptm) cc_final: 0.8461 (ptt)
REVERT: A  314 ASP cc_start: 0.8254 (t0) cc_final: 0.7731 (m-30)
REVERT: A  491 MET cc_start: 0.8544 (mmp) cc_final: 0.8125 (mmt)
REVERT: C   90 MET cc_start: 0.8784 (ptm) cc_final: 0.8488 (ptt)
REVERT: C  314 ASP cc_start: 0.8364 (t0) cc_final: 0.7814 (m-30)
  outliers start: 16
  outliers final: 9
  residues processed: 133
  average time/residue: 0.2815
  time to fit residues: 47.9364
Evaluate side-chains
  108 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
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  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 55 optimal weight:    0.0770
   chunk 58 optimal weight:    4.9990
   chunk 77 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 96 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 95 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.1742

-------------------------------------------------------------------------------
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 = 0.3731 r_free = 0.3731 target = 0.156537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.120900 restraints weight = 9976.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 1.75
r_work: 0.3048 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8623  Z= 0.226
  Angle     :  0.600   6.923  11693  Z= 0.308
  Chirality :  0.042   0.174   1391
  Planarity :  0.004   0.036   1434
  Dihedral  :  4.928  37.410   1196
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  :  6.75 %
    Favored  : 90.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.61 (0.23), residues: 1064
  helix: -1.94 (0.19), residues: 552
  sheet: -3.50 (0.51), residues: 84
  loop : -2.61 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 426 
 HIS   0.006   0.001   HIS C 219 
 PHE   0.030   0.002   PHE A 502 
 TYR   0.014   0.002   TYR A 586 
 ARG   0.003   0.001   ARG A 431 

*********************** 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
  130 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A   90 MET cc_start: 0.8749 (ptm) cc_final: 0.8401 (ptt)
REVERT: A  314 ASP cc_start: 0.8264 (t0) cc_final: 0.7712 (m-30)
REVERT: A  531 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.8847 (tt0)
REVERT: C   90 MET cc_start: 0.8781 (ptm) cc_final: 0.8440 (ptt)
REVERT: C  314 ASP cc_start: 0.8295 (t0) cc_final: 0.7675 (m-30)
REVERT: C  531 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.8863 (tt0)
  outliers start: 27
  outliers final: 22
  residues processed: 123
  average time/residue: 0.2807
  time to fit residues: 44.5144
Evaluate side-chains
  117 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
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  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  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  187 SER
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 53 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 105 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 60 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3698 r_free = 0.3698 target = 0.154119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.118325 restraints weight = 9950.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 1.77
r_work: 0.3000 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.2966

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= 0.192
  Angle     :  0.555   6.681  11693  Z= 0.284
  Chirality :  0.041   0.144   1391
  Planarity :  0.004   0.037   1434
  Dihedral  :  4.704  36.219   1196
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  :  7.08 %
    Favored  : 89.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.19 (0.23), residues: 1064
  helix: -1.43 (0.21), residues: 570
  sheet: -3.01 (0.52), residues: 84
  loop : -2.79 (0.27), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 426 
 HIS   0.006   0.001   HIS C 219 
 PHE   0.030   0.001   PHE A 502 
 TYR   0.012   0.001   TYR A 508 
 ARG   0.004   0.000   ARG C 158 

*********************** 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
  133 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 0.957 
Fit side-chains
REVERT: A   90 MET cc_start: 0.8751 (ptm) cc_final: 0.8448 (ptt)
REVERT: A  179 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7327 (mp)
REVERT: A  314 ASP cc_start: 0.8276 (t0) cc_final: 0.7756 (m-30)
REVERT: A  531 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.9020 (tt0)
REVERT: C   90 MET cc_start: 0.8760 (ptm) cc_final: 0.8453 (ptt)
REVERT: C  314 ASP cc_start: 0.8264 (t0) cc_final: 0.7672 (m-30)
REVERT: C  531 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.9024 (tt0)
  outliers start: 30
  outliers final: 24
  residues processed: 125
  average time/residue: 0.2752
  time to fit residues: 44.5304
Evaluate side-chains
  120 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 93
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
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  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  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  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
Chi-restraints excluded: chain C residue  633 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0010
   chunk 63 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 71 optimal weight:    0.0070
   chunk 36 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 76 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.9808

-------------------------------------------------------------------------------
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 = 0.3658 r_free = 0.3658 target = 0.151077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.114192 restraints weight = 9970.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 1.87
r_work: 0.3010 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.3168

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= 0.192
  Angle     :  0.550   6.678  11693  Z= 0.281
  Chirality :  0.041   0.143   1391
  Planarity :  0.004   0.038   1434
  Dihedral  :  4.617  35.677   1196
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  :  7.63 %
    Favored  : 88.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.80 (0.24), residues: 1064
  helix: -1.07 (0.21), residues: 570
  sheet: -2.95 (0.51), residues: 84
  loop : -2.64 (0.27), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 426 
 HIS   0.006   0.001   HIS A 219 
 PHE   0.021   0.001   PHE C 502 
 TYR   0.011   0.001   TYR A 586 
 ARG   0.004   0.000   ARG C 158 

*********************** 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: 35
    poor density    : 96
  time to evaluate  : 0.845 
Fit side-chains
REVERT: A   90 MET cc_start: 0.8824 (ptm) cc_final: 0.8533 (ptt)
REVERT: A  179 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7455 (mp)
REVERT: A  314 ASP cc_start: 0.8368 (t0) cc_final: 0.7832 (m-30)
REVERT: A  474 MET cc_start: 0.9089 (mtp) cc_final: 0.8820 (mtp)
REVERT: A  531 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.9025 (tt0)
REVERT: C   90 MET cc_start: 0.8758 (ptm) cc_final: 0.8452 (ptt)
REVERT: C  179 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7299 (mp)
REVERT: C  314 ASP cc_start: 0.8361 (t0) cc_final: 0.7814 (m-30)
REVERT: C  474 MET cc_start: 0.9109 (mtp) cc_final: 0.8850 (mtp)
REVERT: C  531 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.9028 (tt0)
  outliers start: 35
  outliers final: 27
  residues processed: 123
  average time/residue: 0.2442
  time to fit residues: 39.6457
Evaluate side-chains
  125 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 94
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
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  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  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  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  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
Chi-restraints excluded: chain C residue  633 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 91 optimal weight:    0.6980
   chunk 77 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 98 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 78 optimal weight:    0.0050
   overall best weight:    0.6796

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.152612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.115927 restraints weight = 9891.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 1.86
r_work: 0.2984 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.3347

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= 0.150
  Angle     :  0.512   6.567  11693  Z= 0.263
  Chirality :  0.040   0.141   1391
  Planarity :  0.003   0.038   1434
  Dihedral  :  4.399  34.457   1196
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  :  8.17 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.39 (0.25), residues: 1064
  helix: -0.66 (0.22), residues: 562
  sheet: -2.70 (0.52), residues: 84
  loop : -2.56 (0.27), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 426 
 HIS   0.004   0.001   HIS A 219 
 PHE   0.022   0.001   PHE A 502 
 TYR   0.008   0.001   TYR A 586 
 ARG   0.004   0.000   ARG C 158 

*********************** 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: 36
    poor density    : 100
  time to evaluate  : 0.842 
Fit side-chains
REVERT: A   90 MET cc_start: 0.8834 (ptm) cc_final: 0.8547 (ptt)
REVERT: A  179 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7414 (mp)
REVERT: A  314 ASP cc_start: 0.8316 (t0) cc_final: 0.7777 (m-30)
REVERT: A  431 ARG cc_start: 0.8522 (ptp-110) cc_final: 0.8139 (mtt90)
REVERT: C   90 MET cc_start: 0.8772 (ptm) cc_final: 0.8472 (ptt)
REVERT: C  179 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7260 (mp)
REVERT: C  314 ASP cc_start: 0.8326 (t0) cc_final: 0.7758 (m-30)
REVERT: C  431 ARG cc_start: 0.8525 (ptp-110) cc_final: 0.8217 (mtm-85)
  outliers start: 36
  outliers final: 25
  residues processed: 129
  average time/residue: 0.2491
  time to fit residues: 42.5541
Evaluate side-chains
  123 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 96
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
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  174 THR
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  340 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain A residue  633 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  174 THR
Chi-restraints excluded: chain C residue  179 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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0570
   chunk 107 optimal weight:    1.9990
   chunk 88 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    0.7102

-------------------------------------------------------------------------------
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 = 0.3604 r_free = 0.3604 target = 0.148204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.111173 restraints weight = 10038.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 1.77
r_work: 0.2979 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2847 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.3460

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= 0.154
  Angle     :  0.512   6.567  11693  Z= 0.262
  Chirality :  0.040   0.137   1391
  Planarity :  0.003   0.038   1434
  Dihedral  :  4.333  34.578   1196
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  :  9.80 %
    Favored  : 86.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.25), residues: 1064
  helix: -0.48 (0.22), residues: 562
  sheet: -3.11 (0.48), residues: 92
  loop : -2.29 (0.28), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 426 
 HIS   0.005   0.001   HIS C 219 
 PHE   0.011   0.001   PHE C 499 
 TYR   0.009   0.001   TYR A 586 
 ARG   0.004   0.000   ARG C 158 

*********************** 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
  130 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 100
  time to evaluate  : 0.976 
Fit side-chains
REVERT: A   90 MET cc_start: 0.8823 (ptm) cc_final: 0.8540 (ptt)
REVERT: A  179 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7431 (mp)
REVERT: A  285 LYS cc_start: 0.8707 (mppt) cc_final: 0.8457 (mppt)
REVERT: A  314 ASP cc_start: 0.8328 (t0) cc_final: 0.7866 (m-30)
REVERT: A  431 ARG cc_start: 0.8512 (ptp-110) cc_final: 0.8182 (mtt90)
REVERT: C   90 MET cc_start: 0.8817 (ptm) cc_final: 0.8530 (ptt)
REVERT: C  179 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7288 (mp)
REVERT: C  314 ASP cc_start: 0.8384 (t0) cc_final: 0.7892 (m-30)
REVERT: C  431 ARG cc_start: 0.8469 (ptp-110) cc_final: 0.8148 (mtt90)
  outliers start: 30
  outliers final: 26
  residues processed: 123
  average time/residue: 0.2693
  time to fit residues: 43.6434
Evaluate side-chains
  128 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
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  139 LEU
Chi-restraints excluded: chain A residue  174 THR
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  340 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain C residue   38 ILE
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  197 THR
Chi-restraints excluded: chain C residue  235 SER
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 80 optimal weight:    0.1980
   chunk 96 optimal weight:    0.5980
   chunk 3 optimal weight:    5.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3671 r_free = 0.3671 target = 0.153144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.116588 restraints weight = 10038.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 1.78
r_work: 0.2983 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.3530

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= 0.155
  Angle     :  0.509   6.543  11693  Z= 0.261
  Chirality :  0.040   0.132   1391
  Planarity :  0.003   0.038   1434
  Dihedral  :  4.306  34.111   1196
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  :  9.69 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.25), residues: 1064
  helix: -0.33 (0.22), residues: 562
  sheet: -2.97 (0.49), residues: 92
  loop : -2.21 (0.28), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 426 
 HIS   0.005   0.001   HIS C 219 
 PHE   0.011   0.001   PHE A 499 
 TYR   0.009   0.001   TYR C 586 
 ARG   0.004   0.000   ARG C 158 

*********************** 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
  133 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 101
  time to evaluate  : 0.906 
Fit side-chains
REVERT: A   90 MET cc_start: 0.8805 (ptm) cc_final: 0.8518 (ptt)
REVERT: A  179 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7419 (mp)
REVERT: A  314 ASP cc_start: 0.8358 (t0) cc_final: 0.7876 (m-30)
REVERT: A  431 ARG cc_start: 0.8541 (ptp-110) cc_final: 0.8192 (mtt90)
REVERT: C   90 MET cc_start: 0.8830 (ptm) cc_final: 0.8551 (ptt)
REVERT: C  179 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7323 (mp)
REVERT: C  314 ASP cc_start: 0.8363 (t0) cc_final: 0.7869 (m-30)
REVERT: C  431 ARG cc_start: 0.8474 (ptp-110) cc_final: 0.8167 (mtt90)
  outliers start: 32
  outliers final: 27
  residues processed: 125
  average time/residue: 0.2505
  time to fit residues: 41.4777
Evaluate side-chains
  126 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 97
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
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  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  569 VAL
Chi-restraints excluded: chain A residue  633 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  174 THR
Chi-restraints excluded: chain C residue  179 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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 58 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3536 r_free = 0.3536 target = 0.143979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.106546 restraints weight = 10078.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 1.76
r_work: 0.3006 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2873 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.3608

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= 0.149
  Angle     :  0.504   6.528  11693  Z= 0.258
  Chirality :  0.040   0.131   1391
  Planarity :  0.003   0.037   1434
  Dihedral  :  4.238  33.038   1196
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 10.02 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.25), residues: 1064
  helix: -0.20 (0.22), residues: 564
  sheet: -2.82 (0.50), residues: 92
  loop : -2.08 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 426 
 HIS   0.004   0.001   HIS A 219 
 PHE   0.011   0.001   PHE C 499 
 TYR   0.008   0.001   TYR A 586 
 ARG   0.004   0.000   ARG A 180 

*********************** 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
  129 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 99
  time to evaluate  : 1.054 
Fit side-chains
REVERT: A   90 MET cc_start: 0.8813 (ptm) cc_final: 0.8516 (ptt)
REVERT: A  179 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7430 (mp)
REVERT: A  285 LYS cc_start: 0.8655 (mppt) cc_final: 0.8374 (mppt)
REVERT: A  314 ASP cc_start: 0.8373 (t0) cc_final: 0.7893 (m-30)
REVERT: A  431 ARG cc_start: 0.8531 (ptp-110) cc_final: 0.8188 (mtt90)
REVERT: C   90 MET cc_start: 0.8852 (ptm) cc_final: 0.8581 (ptt)
REVERT: C  179 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7339 (mp)
REVERT: C  285 LYS cc_start: 0.8586 (mppt) cc_final: 0.7917 (mttp)
REVERT: C  314 ASP cc_start: 0.8363 (t0) cc_final: 0.7876 (m-30)
REVERT: C  431 ARG cc_start: 0.8476 (ptp-110) cc_final: 0.8264 (mtm-85)
REVERT: C  474 MET cc_start: 0.9062 (mtp) cc_final: 0.8778 (mtp)
  outliers start: 30
  outliers final: 27
  residues processed: 121
  average time/residue: 0.2675
  time to fit residues: 42.7991
Evaluate side-chains
  127 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
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  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  569 VAL
Chi-restraints excluded: chain A residue  633 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  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  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 47 optimal weight:    0.8980
   chunk 27 optimal weight:    7.9990
   chunk 6 optimal weight:    7.9990
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    1.6784

-------------------------------------------------------------------------------
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 = 0.3488 r_free = 0.3488 target = 0.139810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.105329 restraints weight = 10097.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 1.59
r_work: 0.2908 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8623  Z= 0.295
  Angle     :  0.606   7.079  11693  Z= 0.306
  Chirality :  0.044   0.145   1391
  Planarity :  0.004   0.039   1434
  Dihedral  :  4.694  33.347   1196
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 10.57 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.24), residues: 1064
  helix: -0.55 (0.21), residues: 570
  sheet: -2.47 (0.56), residues: 80
  loop : -2.25 (0.27), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 426 
 HIS   0.008   0.001   HIS C 219 
 PHE   0.012   0.002   PHE C 583 
 TYR   0.012   0.001   TYR A 586 
 ARG   0.004   0.001   ARG C 158 

********************** 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
  128 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 0.924 
Fit side-chains
REVERT: A   90 MET cc_start: 0.8803 (ptm) cc_final: 0.8519 (ptt)
REVERT: A  140 LYS cc_start: 0.7632 (mtmp) cc_final: 0.7366 (ptpp)
REVERT: A  179 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7435 (mp)
REVERT: A  285 LYS cc_start: 0.8719 (mppt) cc_final: 0.8441 (mppt)
REVERT: A  314 ASP cc_start: 0.8336 (t0) cc_final: 0.7883 (m-30)
REVERT: A  431 ARG cc_start: 0.8600 (ptp-110) cc_final: 0.8306 (mtm-85)
REVERT: C   90 MET cc_start: 0.8813 (ptm) cc_final: 0.8542 (ptt)
REVERT: C  179 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7477 (mp)
REVERT: C  314 ASP cc_start: 0.8322 (t0) cc_final: 0.7864 (m-30)
REVERT: C  431 ARG cc_start: 0.8592 (ptp-110) cc_final: 0.8343 (mtm-85)
  outliers start: 29
  outliers final: 26
  residues processed: 120
  average time/residue: 0.2571
  time to fit residues: 40.3924
Evaluate side-chains
  126 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 98
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
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  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  569 VAL
Chi-restraints excluded: chain A residue  633 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  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  408 LEU
Chi-restraints excluded: chain C residue  450 LEU
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 28 optimal weight:    9.9990
   chunk 49 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 88 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0000
   overall best weight:    0.6384

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.156278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.120423 restraints weight = 10047.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 1.73
r_work: 0.3007 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.3706

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= 0.147
  Angle     :  0.508   6.757  11693  Z= 0.261
  Chirality :  0.040   0.137   1391
  Planarity :  0.003   0.037   1434
  Dihedral  :  4.304  32.406   1196
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 10.89 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.25), residues: 1064
  helix: -0.14 (0.22), residues: 562
  sheet: -2.75 (0.51), residues: 92
  loop : -2.04 (0.28), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 426 
 HIS   0.005   0.001   HIS A 219 
 PHE   0.011   0.001   PHE C 499 
 TYR   0.008   0.001   TYR A 586 
 ARG   0.004   0.000   ARG A 180 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4384.88 seconds
wall clock time: 78 minutes 16.51 seconds (4696.51 seconds total)