Starting phenix.real_space_refine
on Thu Feb 13 00:23:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k0z_36781/02_2025/8k0z_36781.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k0z_36781/02_2025/8k0z_36781.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k0z_36781/02_2025/8k0z_36781.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k0z_36781/02_2025/8k0z_36781.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k0z_36781/02_2025/8k0z_36781.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k0z_36781/02_2025/8k0z_36781.cif"
  }
  resolution = 3.7
  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=   0.006 sd=   0.101
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    5524      2.51       5
     N    1416      2.21       5
     O    1492      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: 8484
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4242
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 546, 4242
          Classifications: {'peptide': 546}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 527}
          Chain breaks: 4
  Restraints were copied for chains:
    B
  Time building chain proxies: 6.80, per 1000 atoms: 0.80
  Number of scatterers: 8484
  At special positions: 0
  Unit cell: (108.9, 73.7, 122.1, 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    1492      8.00
     N    1416      7.00
     C    5524      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: 1.91
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2004

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 6 sheets defined
      57.5% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 106 through 116
      removed outlier: 3.579A  pdb=" N   LEU A 110 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LEU A 111 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 140
      removed outlier: 3.763A  pdb=" N   LYS A 140 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 169
    Processing helix  chain 'A' and resid 175 through 180
      removed outlier: 3.679A  pdb=" N   LEU A 179 " --> pdb=" O   ARG A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 219
      removed outlier: 3.732A  pdb=" N   SER A 216 " --> pdb=" O   ARG A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 255
      removed outlier: 3.813A  pdb=" N   VAL A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 275
      removed outlier: 3.644A  pdb=" N   MET A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   PHE A 275 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 270 through 275'
    Processing helix  chain 'A' and resid 295 through 303
      removed outlier: 3.614A  pdb=" N   PHE A 299 " --> pdb=" O   ALA A 295 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLU A 300 " --> pdb=" O   MET A 296 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   SER A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL A 302 " --> pdb=" O   TYR A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 320
      removed outlier: 3.652A  pdb=" N   LEU A 316 " --> pdb=" O   PRO A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 349
      removed outlier: 3.722A  pdb=" N   VAL A 342 " --> pdb=" O   ARG A 338 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   THR A 347 " --> pdb=" O   THR A 343 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU A 348 " --> pdb=" O   ALA A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 356
      removed outlier: 3.516A  pdb=" N   LYS A 354 " --> pdb=" O   ALA A 350 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   THR A 355 " --> pdb=" O   PRO A 351 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   CYS A 356 " --> pdb=" O   GLN A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 397
      removed outlier: 4.210A  pdb=" N   TRP A 386 " --> pdb=" O   CYS A 382 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   HIS A 395 " --> pdb=" O   CYS A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 406
      removed outlier: 3.515A  pdb=" N   ARG A 402 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   HIS A 403 " --> pdb=" O   LYS A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 425
      removed outlier: 3.512A  pdb=" N   PHE A 412 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   GLN A 413 " --> pdb=" O   LEU A 409 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL A 414 " --> pdb=" O   ARG A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 454
      removed outlier: 3.615A  pdb=" N   ARG A 436 " --> pdb=" O   ASP A 432 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLY A 438 " --> pdb=" O   HIS A 434 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   SER A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLY A 448 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
      removed outlier: 3.764A  pdb=" N   ASN A 454 " --> pdb=" O   LEU A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 462
      removed outlier: 3.683A  pdb=" N   GLN A 461 " --> pdb=" O   PHE A 457 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLU A 462 " --> pdb=" O   THR A 458 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 457 through 462'
    Processing helix  chain 'A' and resid 463 through 472
      removed outlier: 3.552A  pdb=" N   ALA A 471 " --> pdb=" O   THR A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 492
      removed outlier: 3.617A  pdb=" N   MET A 482 " --> pdb=" O   SER A 478 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA A 483 " --> pdb=" O   SER A 479 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   HIS A 484 " --> pdb=" O   TYR A 480 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLY A 487 " --> pdb=" O   ALA A 483 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   SER A 490 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   MET A 491 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 504
      removed outlier: 3.505A  pdb=" N   LEU A 500 " --> pdb=" O   PRO A 496 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR A 501 " --> pdb=" O   ALA A 497 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE A 502 " --> pdb=" O   SER A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 542
      removed outlier: 3.549A  pdb=" N   PHE A 516 " --> pdb=" O   GLY A 512 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   SER A 521 " --> pdb=" O   LEU A 517 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY A 532 " --> pdb=" O   LEU A 528 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   GLY A 534 " --> pdb=" O   SER A 530 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE A 541 " --> pdb=" O   LEU A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 561
    Processing helix  chain 'A' and resid 575 through 579
      removed outlier: 3.687A  pdb=" N   VAL A 579 " --> pdb=" O   MET A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 594
      removed outlier: 3.879A  pdb=" N   TYR A 584 " --> pdb=" O   SER A 580 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU A 588 " --> pdb=" O   TYR A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 631
      removed outlier: 3.943A  pdb=" N   GLY A 631 " --> pdb=" O   GLU A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 658
      removed outlier: 3.723A  pdb=" N   VAL A 639 " --> pdb=" O   MET A 635 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   VAL A 641 " --> pdb=" O   THR A 637 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   TYR A 649 " --> pdb=" O   MET A 645 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ARG A 650 " --> pdb=" O   PHE A 646 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA A 656 " --> pdb=" O   LEU A 652 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 116
      removed outlier: 3.578A  pdb=" N   LEU B 110 " --> pdb=" O   GLY B 106 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LEU B 111 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 140
      removed outlier: 3.763A  pdb=" N   LYS B 140 " --> pdb=" O   LYS B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 169
    Processing helix  chain 'B' and resid 175 through 180
      removed outlier: 3.679A  pdb=" N   LEU B 179 " --> pdb=" O   ARG B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 219
      removed outlier: 3.732A  pdb=" N   SER B 216 " --> pdb=" O   ARG B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 255
      removed outlier: 3.813A  pdb=" N   VAL B 246 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA B 253 " --> pdb=" O   LEU B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 275
      removed outlier: 3.643A  pdb=" N   MET B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   PHE B 275 " --> pdb=" O   VAL B 271 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 270 through 275'
    Processing helix  chain 'B' and resid 295 through 303
      removed outlier: 3.615A  pdb=" N   PHE B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLU B 300 " --> pdb=" O   MET B 296 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   SER B 301 " --> pdb=" O   ALA B 297 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL B 302 " --> pdb=" O   TYR B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 311 through 320
      removed outlier: 3.652A  pdb=" N   LEU B 316 " --> pdb=" O   PRO B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 349
      removed outlier: 3.722A  pdb=" N   VAL B 342 " --> pdb=" O   ARG B 338 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   THR B 347 " --> pdb=" O   THR B 343 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU B 348 " --> pdb=" O   ALA B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 356
      removed outlier: 3.517A  pdb=" N   LYS B 354 " --> pdb=" O   ALA B 350 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   THR B 355 " --> pdb=" O   PRO B 351 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   CYS B 356 " --> pdb=" O   GLN B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 397
      removed outlier: 4.210A  pdb=" N   TRP B 386 " --> pdb=" O   CYS B 382 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   HIS B 395 " --> pdb=" O   CYS B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 406
      removed outlier: 3.516A  pdb=" N   ARG B 402 " --> pdb=" O   LEU B 398 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   HIS B 403 " --> pdb=" O   LYS B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 425
      removed outlier: 3.513A  pdb=" N   PHE B 412 " --> pdb=" O   LEU B 408 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   GLN B 413 " --> pdb=" O   LEU B 409 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL B 414 " --> pdb=" O   ARG B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 454
      removed outlier: 3.615A  pdb=" N   ARG B 436 " --> pdb=" O   ASP B 432 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLY B 438 " --> pdb=" O   HIS B 434 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   SER B 444 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLY B 448 " --> pdb=" O   SER B 444 " (cutoff:3.500A)
      Proline residue:  B 451  - end of helix
      removed outlier: 3.765A  pdb=" N   ASN B 454 " --> pdb=" O   LEU B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 462
      removed outlier: 3.682A  pdb=" N   GLN B 461 " --> pdb=" O   PHE B 457 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLU B 462 " --> pdb=" O   THR B 458 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 457 through 462'
    Processing helix  chain 'B' and resid 463 through 472
      removed outlier: 3.553A  pdb=" N   ALA B 471 " --> pdb=" O   THR B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 492
      removed outlier: 3.618A  pdb=" N   MET B 482 " --> pdb=" O   SER B 478 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA B 483 " --> pdb=" O   SER B 479 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   HIS B 484 " --> pdb=" O   TYR B 480 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLY B 487 " --> pdb=" O   ALA B 483 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   SER B 490 " --> pdb=" O   LEU B 486 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   MET B 491 " --> pdb=" O   GLY B 487 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 504
      removed outlier: 3.505A  pdb=" N   LEU B 500 " --> pdb=" O   PRO B 496 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR B 501 " --> pdb=" O   ALA B 497 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE B 502 " --> pdb=" O   SER B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 542
      removed outlier: 3.548A  pdb=" N   PHE B 516 " --> pdb=" O   GLY B 512 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   SER B 521 " --> pdb=" O   LEU B 517 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY B 532 " --> pdb=" O   LEU B 528 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   LEU B 533 " --> pdb=" O   ALA B 529 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLY B 534 " --> pdb=" O   SER B 530 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE B 541 " --> pdb=" O   LEU B 537 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 549 through 561
    Processing helix  chain 'B' and resid 575 through 579
      removed outlier: 3.687A  pdb=" N   VAL B 579 " --> pdb=" O   MET B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 580 through 594
      removed outlier: 3.878A  pdb=" N   TYR B 584 " --> pdb=" O   SER B 580 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU B 588 " --> pdb=" O   TYR B 584 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 627 through 631
      removed outlier: 3.943A  pdb=" N   GLY B 631 " --> pdb=" O   GLU B 628 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 635 through 658
      removed outlier: 3.722A  pdb=" N   VAL B 639 " --> pdb=" O   MET B 635 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   VAL B 641 " --> pdb=" O   THR B 637 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   TYR B 649 " --> pdb=" O   MET B 645 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ARG B 650 " --> pdb=" O   PHE B 646 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA B 656 " --> pdb=" O   LEU B 652 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 91
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47
      removed outlier: 5.443A  pdb=" N   VAL A  45 " --> pdb=" O   GLY A  86 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU A  84 " --> pdb=" O   TYR A  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145
      removed outlier: 6.416A  pdb=" N   GLY A 143 " --> pdb=" O   VAL A 229 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   LEU A 228 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   MET A  97 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   VAL A 278 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   VAL A 289 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   LEU A 280 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 91
    Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 47
      removed outlier: 5.444A  pdb=" N   VAL B  45 " --> pdb=" O   GLY B  86 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU B  84 " --> pdb=" O   TYR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 142 through 145
      removed outlier: 6.414A  pdb=" N   GLY B 143 " --> pdb=" O   VAL B 229 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   LEU B 228 " --> pdb=" O   VAL B 261 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   MET B  97 " --> pdb=" O   THR B 262 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   VAL B 278 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   VAL B 289 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   LEU B 280 " --> pdb=" O   LEU B 287 " (cutoff:3.500A)

    336 hydrogen bonds defined for protein.
    978 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: 2.39

  Time building geometry restraints manager: 2.24 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: 2604
        1.34 -     1.46: 1753
        1.46 -     1.58: 4219
        1.58 -     1.70: 0
        1.70 -     1.81: 84
  Bond restraints: 8660
  Sorted by residual:
  bond pdb=" CB  PRO A 451 "
       pdb=" CG  PRO A 451 "
    ideal  model  delta    sigma   weight residual
    1.492  1.401  0.091 5.00e-02 4.00e+02 3.28e+00
  bond pdb=" CB  PRO B 451 "
       pdb=" CG  PRO B 451 "
    ideal  model  delta    sigma   weight residual
    1.492  1.402  0.090 5.00e-02 4.00e+02 3.24e+00
  bond pdb=" CG  LEU B 509 "
       pdb=" CD2 LEU B 509 "
    ideal  model  delta    sigma   weight residual
    1.521  1.462  0.059 3.30e-02 9.18e+02 3.18e+00
  bond pdb=" CG  LEU A 509 "
       pdb=" CD2 LEU A 509 "
    ideal  model  delta    sigma   weight residual
    1.521  1.463  0.058 3.30e-02 9.18e+02 3.13e+00
  bond pdb=" CB  VAL A 185 "
       pdb=" CG1 VAL A 185 "
    ideal  model  delta    sigma   weight residual
    1.521  1.463  0.058 3.30e-02 9.18e+02 3.07e+00
  ... (remaining 8655 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.64: 11362
        2.64 -     5.27: 328
        5.27 -     7.91: 38
        7.91 -    10.54: 10
       10.54 -    13.18: 2
  Bond angle restraints: 11740
  Sorted by residual:
  angle pdb=" N   VAL B 185 "
        pdb=" CA  VAL B 185 "
        pdb=" C   VAL B 185 "
      ideal   model   delta    sigma   weight residual
     112.96  107.28    5.68 1.00e+00 1.00e+00 3.23e+01
  angle pdb=" N   VAL A 185 "
        pdb=" CA  VAL A 185 "
        pdb=" C   VAL A 185 "
      ideal   model   delta    sigma   weight residual
     112.96  107.31    5.65 1.00e+00 1.00e+00 3.20e+01
  angle pdb=" N   SER B 571 "
        pdb=" CA  SER B 571 "
        pdb=" C   SER B 571 "
      ideal   model   delta    sigma   weight residual
     110.80  119.37   -8.57 2.13e+00 2.20e-01 1.62e+01
  angle pdb=" N   SER A 571 "
        pdb=" CA  SER A 571 "
        pdb=" C   SER A 571 "
      ideal   model   delta    sigma   weight residual
     110.80  119.35   -8.55 2.13e+00 2.20e-01 1.61e+01
  angle pdb=" CB  ARG B 436 "
        pdb=" CG  ARG B 436 "
        pdb=" CD  ARG B 436 "
      ideal   model   delta    sigma   weight residual
     111.30  120.21   -8.91 2.30e+00 1.89e-01 1.50e+01
  ... (remaining 11735 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.02: 4828
       15.02 -    30.04: 211
       30.04 -    45.06: 39
       45.06 -    60.07: 6
       60.07 -    75.09: 6
  Dihedral angle restraints: 5090
    sinusoidal: 1968
      harmonic: 3122
  Sorted by residual:
  dihedral pdb=" CA  VAL B 177 "
           pdb=" C   VAL B 177 "
           pdb=" N   LYS B 178 "
           pdb=" CA  LYS B 178 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.40   24.60     0      5.00e+00 4.00e-02 2.42e+01
  dihedral pdb=" CA  VAL A 177 "
           pdb=" C   VAL A 177 "
           pdb=" N   LYS A 178 "
           pdb=" CA  LYS A 178 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.42   24.58     0      5.00e+00 4.00e-02 2.42e+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  155.76   24.24     0      5.00e+00 4.00e-02 2.35e+01
  ... (remaining 5087 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 928
       0.058 -    0.115: 393
       0.115 -    0.172: 63
       0.172 -    0.230: 12
       0.230 -    0.287: 4
  Chirality restraints: 1400
  Sorted by residual:
  chirality pdb=" CB  VAL A 177 "
            pdb=" CA  VAL A 177 "
            pdb=" CG1 VAL A 177 "
            pdb=" CG2 VAL A 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.07e+00
  chirality pdb=" CB  VAL B 177 "
            pdb=" CA  VAL B 177 "
            pdb=" CG1 VAL B 177 "
            pdb=" CG2 VAL B 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" CB  ILE B 630 "
            pdb=" CA  ILE B 630 "
            pdb=" CG1 ILE B 630 "
            pdb=" CG2 ILE B 630 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.90   -0.26 2.00e-01 2.50e+01 1.68e+00
  ... (remaining 1397 not shown)

  Planarity restraints: 1440
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 450 "    0.040 5.00e-02 4.00e+02   6.01e-02 5.78e+00
        pdb=" N   PRO A 451 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 451 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 451 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 450 "   -0.040 5.00e-02 4.00e+02   5.97e-02 5.70e+00
        pdb=" N   PRO B 451 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO B 451 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 451 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 350 "   -0.035 5.00e-02 4.00e+02   5.28e-02 4.46e+00
        pdb=" N   PRO A 351 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 351 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 351 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1437 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 2935
        2.87 -     3.38: 7214
        3.38 -     3.89: 12545
        3.89 -     4.39: 15057
        4.39 -     4.90: 26518
  Nonbonded interactions: 64269
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 298 "
            pdb=" OG  SER B 301 "
     model   vdw
     2.364 3.040
  nonbonded pdb=" O   TYR A 298 "
            pdb=" OG  SER A 301 "
     model   vdw
     2.364 3.040
  nonbonded pdb=" N   GLY A 572 "
            pdb=" N   MET A 573 "
     model   vdw
     2.423 2.560
  nonbonded pdb=" OG  SER B 452 "
            pdb=" O   SER B 530 "
     model   vdw
     2.423 3.040
  nonbonded pdb=" OG  SER A 452 "
            pdb=" O   SER A 530 "
     model   vdw
     2.424 3.040
  ... (remaining 64264 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.470
  Find NCS groups from input model:        0.140
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
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      :  0.010   0.091   8660  Z= 0.660
  Angle     :  1.063  13.178  11740  Z= 0.561
  Chirality :  0.062   0.287   1400
  Planarity :  0.007   0.060   1440
  Dihedral  :  9.688  75.092   3086
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.84 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  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: -6.16 (0.16), residues: 1072
  helix: -4.85 (0.06), residues: 588
  sheet: -1.12 (0.62), residues: 62
  loop : -3.10 (0.25), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.004   TRP B 447 
 HIS   0.013   0.003   HIS A 219 
 PHE   0.027   0.004   PHE B 163 
 TYR   0.023   0.003   TYR A 526 
 ARG   0.017   0.001   ARG B 436 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.891 
Fit side-chains
REVERT: A   87 VAL cc_start: 0.8387 (t) cc_final: 0.8124 (t)
REVERT: A  105 SER cc_start: 0.9055 (p) cc_final: 0.8675 (t)
REVERT: B   87 VAL cc_start: 0.8350 (t) cc_final: 0.8096 (t)
REVERT: B  105 SER cc_start: 0.9063 (p) cc_final: 0.8659 (t)
REVERT: B  294 ASP cc_start: 0.8217 (p0) cc_final: 0.7994 (p0)
REVERT: B  454 ASN cc_start: 0.8619 (m110) cc_final: 0.8114 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.2943
  time to fit residues: 81.4207
Evaluate side-chains
  125 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 81 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:   10.0000
   chunk 55 optimal weight:    7.9990
   chunk 43 optimal weight:    0.6980
   chunk 84 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 63 optimal weight:    0.6980
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 219 HIS
A 427 HIS
A 531 GLN
B 219 HIS
B 531 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.142153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.105983 restraints weight = 11285.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.106227 restraints weight = 11335.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.107406 restraints weight = 9906.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   8660  Z= 0.187
  Angle     :  0.634   7.253  11740  Z= 0.328
  Chirality :  0.042   0.153   1400
  Planarity :  0.005   0.038   1440
  Dihedral  :  5.398  47.593   1180
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  6.70 %
    Favored  : 91.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -4.11 (0.21), residues: 1072
  helix: -2.74 (0.16), residues: 590
  sheet: -0.67 (0.64), residues: 62
  loop : -2.83 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 447 
 HIS   0.005   0.001   HIS A 219 
 PHE   0.018   0.002   PHE B  42 
 TYR   0.010   0.001   TYR A 508 
 ARG   0.004   0.000   ARG A 180 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 150
  time to evaluate  : 0.944 
Fit side-chains
REVERT: A  105 SER cc_start: 0.9268 (p) cc_final: 0.9055 (t)
REVERT: A  232 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7783 (tp30)
REVERT: A  454 ASN cc_start: 0.8925 (m110) cc_final: 0.8592 (m-40)
REVERT: A  482 MET cc_start: 0.7973 (tpp) cc_final: 0.7725 (mmm)
REVERT: A  576 MET cc_start: 0.7980 (ttm) cc_final: 0.7657 (ttp)
REVERT: B  105 SER cc_start: 0.9253 (p) cc_final: 0.9039 (t)
REVERT: B  232 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7796 (tp30)
REVERT: B  319 LEU cc_start: 0.8898 (mp) cc_final: 0.8665 (mp)
REVERT: B  454 ASN cc_start: 0.8926 (m110) cc_final: 0.8481 (m110)
REVERT: B  482 MET cc_start: 0.8023 (tpp) cc_final: 0.7776 (mmm)
REVERT: B  514 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8207 (p)
REVERT: B  576 MET cc_start: 0.8039 (ttm) cc_final: 0.7723 (ttp)
  outliers start: 14
  outliers final: 3
  residues processed: 164
  average time/residue: 0.2105
  time to fit residues: 47.5201
Evaluate side-chains
  120 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 116
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  514 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 55 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   chunk 61 optimal weight:    8.9990
   chunk 96 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 80 optimal weight:    9.9990
   chunk 83 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 247 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.129572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.091304 restraints weight = 11686.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.093535 restraints weight = 8332.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.094826 restraints weight = 6715.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.3987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.044   8660  Z= 0.520
  Angle     :  0.827  10.184  11740  Z= 0.416
  Chirality :  0.050   0.159   1400
  Planarity :  0.005   0.044   1440
  Dihedral  :  5.547  48.471   1180
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  :  9.40 %
    Favored  : 88.01 %
  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: -3.03 (0.23), residues: 1072
  helix: -1.69 (0.20), residues: 598
  sheet: -1.18 (0.62), residues: 62
  loop : -2.46 (0.27), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 447 
 HIS   0.008   0.002   HIS A 434 
 PHE   0.019   0.002   PHE A 646 
 TYR   0.015   0.002   TYR A 475 
 ARG   0.004   0.001   ARG A 470 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 1.057 
Fit side-chains
REVERT: A  247 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7657 (mm-40)
REVERT: A  274 MET cc_start: 0.7781 (mmt) cc_final: 0.7317 (mmt)
REVERT: A  569 VAL cc_start: 0.9134 (t) cc_final: 0.8783 (m)
REVERT: A  636 TRP cc_start: 0.8168 (m100) cc_final: 0.7953 (m-10)
REVERT: B  274 MET cc_start: 0.7800 (mmt) cc_final: 0.7516 (mmt)
REVERT: B  514 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8630 (p)
REVERT: B  569 VAL cc_start: 0.8994 (t) cc_final: 0.8753 (m)
REVERT: B  636 TRP cc_start: 0.8164 (m100) cc_final: 0.7942 (m-10)
  outliers start: 24
  outliers final: 14
  residues processed: 140
  average time/residue: 0.2167
  time to fit residues: 41.4592
Evaluate side-chains
  122 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  296 MET
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  514 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 81 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 101 optimal weight:    0.6980
   chunk 2 optimal weight:    8.9990
   chunk 24 optimal weight:    0.9990
   chunk 97 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 389 GLN
B 461 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.142845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.106332 restraints weight = 11420.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.107050 restraints weight = 7457.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.108734 restraints weight = 5900.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.4417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8660  Z= 0.160
  Angle     :  0.585   8.243  11740  Z= 0.295
  Chirality :  0.041   0.130   1400
  Planarity :  0.003   0.040   1440
  Dihedral  :  4.907  43.166   1180
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 12.63 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -2.10 (0.25), residues: 1072
  helix: -0.92 (0.22), residues: 580
  sheet: -0.70 (0.66), residues: 62
  loop : -2.05 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 447 
 HIS   0.002   0.001   HIS A 427 
 PHE   0.015   0.001   PHE B 502 
 TYR   0.008   0.001   TYR B 508 
 ARG   0.003   0.000   ARG B 180 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.951 
Fit side-chains
REVERT: A  232 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8041 (tp30)
REVERT: A  247 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7566 (mm-40)
REVERT: A  274 MET cc_start: 0.7697 (mmt) cc_final: 0.7238 (mmt)
REVERT: A  293 ARG cc_start: 0.7993 (ptp-170) cc_final: 0.7769 (ptp-170)
REVERT: A  319 LEU cc_start: 0.8820 (mp) cc_final: 0.8589 (tt)
REVERT: A  461 GLN cc_start: 0.8055 (mm110) cc_final: 0.7764 (mp10)
REVERT: B  232 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8034 (tp30)
REVERT: B  274 MET cc_start: 0.7723 (mmt) cc_final: 0.7463 (mmt)
REVERT: B  293 ARG cc_start: 0.7973 (ptp-170) cc_final: 0.7750 (ptp-170)
REVERT: B  319 LEU cc_start: 0.8820 (mp) cc_final: 0.8592 (tt)
REVERT: B  461 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7723 (mp10)
REVERT: B  514 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8235 (p)
  outliers start: 15
  outliers final: 10
  residues processed: 132
  average time/residue: 0.2345
  time to fit residues: 41.7764
Evaluate side-chains
  116 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  484 HIS
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  337 VAL
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain B residue  484 HIS
Chi-restraints excluded: chain B residue  514 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 27 optimal weight:   20.0000
   chunk 87 optimal weight:    3.9990
   chunk 92 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   chunk 67 optimal weight:    0.0970
   chunk 45 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.6378

-------------------------------------------------------------------------------
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 = 0.3547 r_free = 0.3547 target = 0.141410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.102208 restraints weight = 11459.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.105495 restraints weight = 7207.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.107663 restraints weight = 5382.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.4651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8660  Z= 0.154
  Angle     :  0.564   8.268  11740  Z= 0.282
  Chirality :  0.040   0.125   1400
  Planarity :  0.003   0.032   1440
  Dihedral  :  4.575  39.744   1180
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 13.07 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.48 (0.26), residues: 1072
  helix: -0.46 (0.22), residues: 582
  sheet: -0.11 (0.70), residues: 62
  loop : -1.75 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 447 
 HIS   0.003   0.001   HIS A 427 
 PHE   0.009   0.001   PHE A 499 
 TYR   0.007   0.001   TYR B 508 
 ARG   0.003   0.000   ARG A 117 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.924 
Fit side-chains
REVERT: A  180 ARG cc_start: 0.7935 (ttm110) cc_final: 0.7601 (ttm110)
REVERT: A  188 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7852 (tm-30)
REVERT: A  232 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8020 (tp30)
REVERT: A  247 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7828 (mm-40)
REVERT: A  274 MET cc_start: 0.7712 (mmt) cc_final: 0.7254 (mmt)
REVERT: A  420 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7969 (mm)
REVERT: A  461 GLN cc_start: 0.8020 (mm110) cc_final: 0.7730 (mp10)
REVERT: A  490 SER cc_start: 0.8755 (m) cc_final: 0.8401 (p)
REVERT: B  232 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7997 (tp30)
REVERT: B  274 MET cc_start: 0.7716 (mmt) cc_final: 0.7431 (mmt)
REVERT: B  420 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7957 (mm)
REVERT: B  461 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7694 (mp10)
REVERT: B  490 SER cc_start: 0.8766 (m) cc_final: 0.8384 (p)
REVERT: B  514 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8223 (p)
  outliers start: 24
  outliers final: 13
  residues processed: 127
  average time/residue: 0.2021
  time to fit residues: 35.8178
Evaluate side-chains
  114 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 ASP
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  484 HIS
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  337 VAL
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  514 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0570
   chunk 35 optimal weight:    0.7980
   chunk 82 optimal weight:    8.9990
   chunk 95 optimal weight:    3.9990
   chunk 54 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 88 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.6300

-------------------------------------------------------------------------------
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 = 0.3574 r_free = 0.3574 target = 0.144037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.105547 restraints weight = 11211.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.108633 restraints weight = 7277.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.110652 restraints weight = 5507.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.4810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8660  Z= 0.161
  Angle     :  0.597  12.729  11740  Z= 0.287
  Chirality :  0.040   0.184   1400
  Planarity :  0.003   0.033   1440
  Dihedral  :  4.482  38.874   1180
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.71 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.09 (0.26), residues: 1072
  helix: -0.15 (0.22), residues: 580
  sheet:  0.23 (0.73), residues: 62
  loop : -1.58 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 447 
 HIS   0.003   0.001   HIS B 427 
 PHE   0.020   0.001   PHE B 502 
 TYR   0.007   0.001   TYR A 508 
 ARG   0.002   0.000   ARG A 658 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.981 
Fit side-chains
REVERT: A   48 ARG cc_start: 0.5600 (tpm170) cc_final: 0.5385 (tpm170)
REVERT: A  188 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7842 (tm-30)
REVERT: A  232 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7991 (tp30)
REVERT: A  247 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7775 (mm-40)
REVERT: A  274 MET cc_start: 0.7694 (mmt) cc_final: 0.7260 (mmt)
REVERT: A  293 ARG cc_start: 0.7950 (ptp-170) cc_final: 0.7743 (ptp-170)
REVERT: A  420 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7958 (mm)
REVERT: A  490 SER cc_start: 0.8751 (m) cc_final: 0.8403 (p)
REVERT: B  188 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7918 (tm-30)
REVERT: B  232 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7989 (tp30)
REVERT: B  274 MET cc_start: 0.7622 (mmt) cc_final: 0.7381 (mmt)
REVERT: B  293 ARG cc_start: 0.7982 (ptp-170) cc_final: 0.7778 (ptp-170)
REVERT: B  420 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7988 (mm)
REVERT: B  461 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7667 (mp10)
REVERT: B  490 SER cc_start: 0.8743 (m) cc_final: 0.8355 (p)
REVERT: B  514 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8199 (p)
  outliers start: 20
  outliers final: 14
  residues processed: 130
  average time/residue: 0.1970
  time to fit residues: 35.7547
Evaluate side-chains
  118 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  484 HIS
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  337 VAL
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  514 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 27 optimal weight:   20.0000
   chunk 107 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 1 optimal weight:    7.9990
   chunk 81 optimal weight:   20.0000
   chunk 32 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 3 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 454 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.135248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.095883 restraints weight = 11702.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.098775 restraints weight = 7620.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.100758 restraints weight = 5819.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.5003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.043   8660  Z= 0.501
  Angle     :  0.806  10.076  11740  Z= 0.393
  Chirality :  0.049   0.156   1400
  Planarity :  0.004   0.032   1440
  Dihedral  :  5.204  47.215   1180
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 13.17 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.26), residues: 1072
  helix: -0.61 (0.21), residues: 596
  sheet: -0.19 (0.71), residues: 62
  loop : -1.76 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 447 
 HIS   0.007   0.002   HIS A 434 
 PHE   0.017   0.002   PHE A 646 
 TYR   0.019   0.002   TYR B 475 
 ARG   0.005   0.001   ARG A 410 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 111
  time to evaluate  : 0.985 
Fit side-chains
REVERT: A  140 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8161 (tppt)
REVERT: A  232 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7976 (tp30)
REVERT: A  274 MET cc_start: 0.7828 (mmt) cc_final: 0.7533 (mmt)
REVERT: A  490 SER cc_start: 0.8952 (m) cc_final: 0.8511 (p)
REVERT: A  636 TRP cc_start: 0.8232 (m100) cc_final: 0.7909 (m-10)
REVERT: B  232 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7975 (tp30)
REVERT: B  274 MET cc_start: 0.7826 (mmt) cc_final: 0.7540 (mmt)
REVERT: B  461 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7766 (mp10)
REVERT: B  490 SER cc_start: 0.8867 (m) cc_final: 0.8507 (p)
REVERT: B  514 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8694 (p)
REVERT: B  636 TRP cc_start: 0.8227 (m100) cc_final: 0.7902 (m-10)
  outliers start: 32
  outliers final: 20
  residues processed: 136
  average time/residue: 0.2036
  time to fit residues: 39.0240
Evaluate side-chains
  124 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 LYS
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  484 HIS
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  337 VAL
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain B residue  514 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 454 ASN
B 454 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.140718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.103850 restraints weight = 11646.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.104039 restraints weight = 7548.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.105222 restraints weight = 6474.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.5130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8660  Z= 0.212
  Angle     :  0.644  10.894  11740  Z= 0.312
  Chirality :  0.042   0.137   1400
  Planarity :  0.003   0.029   1440
  Dihedral  :  4.803  44.038   1180
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.36 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.26), residues: 1072
  helix: -0.25 (0.22), residues: 592
  sheet: -0.03 (0.70), residues: 62
  loop : -1.52 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 447 
 HIS   0.002   0.001   HIS A 434 
 PHE   0.011   0.001   PHE B 499 
 TYR   0.008   0.001   TYR B 475 
 ARG   0.004   0.000   ARG A 602 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.909 
Fit side-chains
REVERT: A  232 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7982 (tp30)
REVERT: A  274 MET cc_start: 0.7686 (mmt) cc_final: 0.7373 (mmt)
REVERT: A  293 ARG cc_start: 0.8073 (ptp-170) cc_final: 0.7822 (ptp-170)
REVERT: A  490 SER cc_start: 0.8837 (m) cc_final: 0.8404 (p)
REVERT: B  232 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8010 (tp30)
REVERT: B  274 MET cc_start: 0.7629 (mmt) cc_final: 0.7374 (mmt)
REVERT: B  293 ARG cc_start: 0.8070 (ptp-170) cc_final: 0.7814 (ptp-170)
REVERT: B  461 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7768 (mp10)
REVERT: B  490 SER cc_start: 0.8788 (m) cc_final: 0.8420 (p)
REVERT: B  514 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8382 (p)
  outliers start: 23
  outliers final: 18
  residues processed: 132
  average time/residue: 0.1954
  time to fit residues: 36.5255
Evaluate side-chains
  127 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  484 HIS
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  337 VAL
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  514 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 63 optimal weight:    0.5980
   chunk 93 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 75 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
B 454 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.137186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.100380 restraints weight = 11656.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.100562 restraints weight = 8067.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.101605 restraints weight = 6125.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.5218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   8660  Z= 0.343
  Angle     :  0.727  11.297  11740  Z= 0.352
  Chirality :  0.045   0.145   1400
  Planarity :  0.004   0.037   1440
  Dihedral  :  4.952  45.824   1180
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.79 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.20 (0.26), residues: 1072
  helix: -0.26 (0.22), residues: 592
  sheet: -0.18 (0.69), residues: 62
  loop : -1.57 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 447 
 HIS   0.005   0.001   HIS A 434 
 PHE   0.014   0.002   PHE B 499 
 TYR   0.014   0.001   TYR A 475 
 ARG   0.009   0.001   ARG A 602 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A  232 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7983 (tp30)
REVERT: A  274 MET cc_start: 0.7795 (mmt) cc_final: 0.7485 (mmt)
REVERT: A  293 ARG cc_start: 0.8127 (ptp-170) cc_final: 0.7853 (ptp-170)
REVERT: A  304 PHE cc_start: 0.7663 (m-80) cc_final: 0.7314 (m-80)
REVERT: A  469 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8040 (mt-10)
REVERT: A  490 SER cc_start: 0.8906 (m) cc_final: 0.8444 (p)
REVERT: B  232 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7985 (tp30)
REVERT: B  274 MET cc_start: 0.7650 (mmt) cc_final: 0.7382 (mmt)
REVERT: B  293 ARG cc_start: 0.8126 (ptp-170) cc_final: 0.7850 (ptp-170)
REVERT: B  304 PHE cc_start: 0.7570 (m-80) cc_final: 0.7282 (m-80)
REVERT: B  461 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7803 (mp10)
REVERT: B  490 SER cc_start: 0.8881 (m) cc_final: 0.8399 (p)
REVERT: B  514 VAL cc_start: 0.8803 (OUTLIER) cc_final: 0.8490 (p)
  outliers start: 24
  outliers final: 21
  residues processed: 131
  average time/residue: 0.2013
  time to fit residues: 37.0955
Evaluate side-chains
  130 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  484 HIS
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  337 VAL
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  514 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 17 optimal weight:    0.6980
   chunk 91 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 43 optimal weight:    0.3980
   chunk 69 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 454 ASN
B 454 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.133990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.095959 restraints weight = 11215.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.097847 restraints weight = 8459.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.099021 restraints weight = 7064.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.5304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8660  Z= 0.225
  Angle     :  0.670  11.893  11740  Z= 0.321
  Chirality :  0.042   0.144   1400
  Planarity :  0.003   0.028   1440
  Dihedral  :  4.790  44.018   1180
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.01 %
    Favored  : 82.72 %
  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: -0.97 (0.26), residues: 1072
  helix: -0.11 (0.22), residues: 596
  sheet:  0.00 (0.69), residues: 62
  loop : -1.42 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 447 
 HIS   0.003   0.001   HIS A 434 
 PHE   0.011   0.001   PHE B 499 
 TYR   0.013   0.001   TYR A 475 
 ARG   0.004   0.000   ARG A  48 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.962 
Fit side-chains
REVERT: A  274 MET cc_start: 0.7658 (mmt) cc_final: 0.7365 (mmt)
REVERT: A  293 ARG cc_start: 0.7957 (ptp-170) cc_final: 0.7703 (ptp-170)
REVERT: A  304 PHE cc_start: 0.7647 (m-80) cc_final: 0.7328 (m-80)
REVERT: A  469 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7954 (mt-10)
REVERT: A  490 SER cc_start: 0.8861 (m) cc_final: 0.8437 (p)
REVERT: B  274 MET cc_start: 0.7661 (mmt) cc_final: 0.7423 (mmt)
REVERT: B  293 ARG cc_start: 0.7950 (ptp-170) cc_final: 0.7669 (ptp-170)
REVERT: B  304 PHE cc_start: 0.7623 (m-80) cc_final: 0.7382 (m-80)
REVERT: B  461 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7758 (mp10)
REVERT: B  490 SER cc_start: 0.8817 (m) cc_final: 0.8412 (p)
REVERT: B  514 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8415 (p)
  outliers start: 21
  outliers final: 19
  residues processed: 128
  average time/residue: 0.1977
  time to fit residues: 35.5453
Evaluate side-chains
  127 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  484 HIS
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  337 VAL
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  514 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 102 optimal weight:    0.4980
   chunk 25 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 454 ASN
B 112 ASN
B 454 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.134306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.097116 restraints weight = 11327.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.098533 restraints weight = 8872.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.099892 restraints weight = 7562.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.5398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8660  Z= 0.217
  Angle     :  0.673  11.789  11740  Z= 0.321
  Chirality :  0.042   0.142   1400
  Planarity :  0.003   0.030   1440
  Dihedral  :  4.713  42.996   1180
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.01 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.26), residues: 1072
  helix:  0.05 (0.22), residues: 596
  sheet:  0.04 (0.68), residues: 62
  loop : -1.35 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 434 
 PHE   0.011   0.001   PHE B 499 
 TYR   0.013   0.001   TYR B 475 
 ARG   0.005   0.000   ARG A 602 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2439.10 seconds
wall clock time: 44 minutes 31.40 seconds (2671.40 seconds total)