Starting phenix.real_space_refine
on Fri Oct 10 18:45:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k0z_36781/10_2025/8k0z_36781.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k0z_36781/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k0z_36781/10_2025/8k0z_36781.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k0z_36781/10_2025/8k0z_36781.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k0z_36781/10_2025/8k0z_36781.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k0z_36781/10_2025/8k0z_36781.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.04, per 1000 atoms: 0.36
  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: 0.57
  Conformation dependent library (CDL) restraints added in 450.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.29
  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: 1.28

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 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: 0.02
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:             0.910
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.620
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.300
-------------------------------------------------------------------------------
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= 0.421
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -6.16 (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
 ARG   0.017   0.001   ARG B 436 
 TYR   0.023   0.003   TYR A 526 
 PHE   0.027   0.004   PHE B 163 
 TRP   0.024   0.004   TRP B 447 
 HIS   0.013   0.003   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.01023 ( 8660)
  covalent geometry    : angle       1.06258 (11740)
  hydrogen bonds       : bond        0.36258 (  336)
  hydrogen bonds       : angle      10.57453 (  978)

*********************** 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  : 0.255 
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: 0.1313
  time to fit residues: 36.2106
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  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.3980
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.5980
   chunk 106 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 427 HIS
B 531 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.143406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.106162 restraints weight = 11442.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.108486 restraints weight = 8279.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.109724 restraints weight = 6722.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.111036 restraints weight = 5911.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.111837 restraints weight = 5395.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.3113

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= 0.116
  Angle     :  0.620   7.713  11740  Z= 0.319
  Chirality :  0.042   0.158   1400
  Planarity :  0.005   0.035   1440
  Dihedral  :  5.329  46.057   1180
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  7.02 %
    Favored  : 91.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.14 (0.21), residues: 1072
  helix: -2.83 (0.16), residues: 590
  sheet: -0.56 (0.65), residues: 62
  loop : -2.76 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 180 
 TYR   0.008   0.001   TYR A 345 
 PHE   0.018   0.002   PHE A  42 
 TRP   0.012   0.001   TRP A 447 
 HIS   0.004   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8660)
  covalent geometry    : angle       0.61986 (11740)
  hydrogen bonds       : bond        0.04470 (  336)
  hydrogen bonds       : angle       4.78551 (  978)

*********************** 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
  170 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 154
  time to evaluate  : 0.543 
Fit side-chains
REVERT: A   42 PHE cc_start: 0.7450 (p90) cc_final: 0.7213 (p90)
REVERT: A  105 SER cc_start: 0.9267 (p) cc_final: 0.9060 (t)
REVERT: A  232 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7862 (tp30)
REVERT: A  288 PHE cc_start: 0.8916 (t80) cc_final: 0.8677 (t80)
REVERT: A  454 ASN cc_start: 0.8947 (m110) cc_final: 0.8633 (m-40)
REVERT: A  482 MET cc_start: 0.7937 (tpp) cc_final: 0.7624 (mmt)
REVERT: A  573 MET cc_start: 0.7775 (tpp) cc_final: 0.7538 (mmt)
REVERT: B  232 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7866 (tp30)
REVERT: B  454 ASN cc_start: 0.8938 (m110) cc_final: 0.8498 (m110)
REVERT: B  482 MET cc_start: 0.7936 (tpp) cc_final: 0.7702 (mmm)
REVERT: B  514 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.8010 (p)
REVERT: B  576 MET cc_start: 0.7939 (ttm) cc_final: 0.7626 (ttp)
  outliers start: 16
  outliers final: 3
  residues processed: 170
  average time/residue: 0.0996
  time to fit residues: 23.6649
Evaluate side-chains
  125 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 121
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
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 16 optimal weight:    4.9990
   chunk 61 optimal weight:    9.9990
   chunk 39 optimal weight:    0.2980
   chunk 74 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 69 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   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 247 GLN
B 247 GLN
B 389 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.144918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.108637 restraints weight = 11173.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.110983 restraints weight = 7896.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.112451 restraints weight = 6350.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.113213 restraints weight = 5521.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.113995 restraints weight = 5066.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.3774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   8660  Z= 0.152
  Angle     :  0.631   8.138  11740  Z= 0.320
  Chirality :  0.042   0.139   1400
  Planarity :  0.004   0.038   1440
  Dihedral  :  4.942  42.710   1180
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 10.58 %
    Favored  : 87.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.39 (0.24), residues: 1072
  helix: -1.20 (0.21), residues: 566
  sheet: -0.48 (0.63), residues: 62
  loop : -2.17 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 180 
 TYR   0.009   0.001   TYR A 475 
 PHE   0.017   0.001   PHE B 315 
 TRP   0.010   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 8660)
  covalent geometry    : angle       0.63126 (11740)
  hydrogen bonds       : bond        0.04985 (  336)
  hydrogen bonds       : angle       4.30447 (  978)

*********************** 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
  143 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.387 
Fit side-chains
REVERT: A  232 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7914 (tp30)
REVERT: A  274 MET cc_start: 0.7489 (mmt) cc_final: 0.7216 (mmt)
REVERT: A  293 ARG cc_start: 0.7710 (ptp-170) cc_final: 0.7478 (ptp-170)
REVERT: A  319 LEU cc_start: 0.8878 (mp) cc_final: 0.8638 (tt)
REVERT: A  454 ASN cc_start: 0.8941 (m110) cc_final: 0.8617 (m-40)
REVERT: A  569 VAL cc_start: 0.8825 (t) cc_final: 0.8424 (m)
REVERT: A  576 MET cc_start: 0.7949 (ttm) cc_final: 0.7706 (ttp)
REVERT: B  180 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7462 (ttm110)
REVERT: B  232 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7920 (tp30)
REVERT: B  274 MET cc_start: 0.7559 (mmt) cc_final: 0.7292 (mmt)
REVERT: B  293 ARG cc_start: 0.7704 (ptp-170) cc_final: 0.7471 (ptp-170)
REVERT: B  319 LEU cc_start: 0.8855 (mp) cc_final: 0.8618 (tt)
REVERT: B  454 ASN cc_start: 0.8926 (m110) cc_final: 0.8550 (m110)
REVERT: B  514 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8257 (p)
  outliers start: 17
  outliers final: 11
  residues processed: 139
  average time/residue: 0.1001
  time to fit residues: 19.2114
Evaluate side-chains
  121 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
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  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  479 SER
Chi-restraints excluded: chain B residue  484 HIS
Chi-restraints excluded: chain B residue  503 THR
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 68 optimal weight:   10.0000
   chunk 78 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 54 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 219 HIS
A 389 GLN
B 219 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.126581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.088538 restraints weight = 11950.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.090556 restraints weight = 8543.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.092103 restraints weight = 6901.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.092927 restraints weight = 6007.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.093589 restraints weight = 5526.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.4579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.053   8660  Z= 0.384
  Angle     :  0.868   9.661  11740  Z= 0.436
  Chirality :  0.053   0.164   1400
  Planarity :  0.005   0.042   1440
  Dihedral  :  5.664  49.686   1180
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 11.12 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.79 (0.24), residues: 1072
  helix: -1.52 (0.20), residues: 608
  sheet: -1.10 (0.64), residues: 62
  loop : -2.31 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 410 
 TYR   0.018   0.003   TYR A 475 
 PHE   0.024   0.002   PHE A 646 
 TRP   0.014   0.002   TRP A 426 
 HIS   0.008   0.002   HIS A 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00939 ( 8660)
  covalent geometry    : angle       0.86831 (11740)
  hydrogen bonds       : bond        0.06539 (  336)
  hydrogen bonds       : angle       4.83811 (  978)

*********************** 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
  141 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 108
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A  201 ASN cc_start: 0.8914 (p0) cc_final: 0.8667 (p0)
REVERT: A  232 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7853 (tp30)
REVERT: A  274 MET cc_start: 0.7858 (mmt) cc_final: 0.7592 (mmt)
REVERT: A  304 PHE cc_start: 0.7516 (m-80) cc_final: 0.7202 (m-80)
REVERT: A  319 LEU cc_start: 0.9058 (mp) cc_final: 0.8773 (tt)
REVERT: B  201 ASN cc_start: 0.8902 (p0) cc_final: 0.8667 (p0)
REVERT: B  232 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7864 (tp30)
REVERT: B  274 MET cc_start: 0.7851 (mmt) cc_final: 0.7525 (mmt)
REVERT: B  304 PHE cc_start: 0.7515 (m-80) cc_final: 0.7229 (m-80)
REVERT: B  319 LEU cc_start: 0.9052 (mp) cc_final: 0.8788 (tt)
REVERT: B  514 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8706 (p)
REVERT: B  569 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8810 (m)
REVERT: B  576 MET cc_start: 0.8047 (ttp) cc_final: 0.7780 (ttm)
  outliers start: 33
  outliers final: 21
  residues processed: 138
  average time/residue: 0.0917
  time to fit residues: 17.4215
Evaluate side-chains
  121 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 PHE
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  148 ASP
Chi-restraints excluded: chain A residue  169 LEU
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  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  128 LEU
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  337 VAL
Chi-restraints excluded: chain B residue  340 THR
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 103 optimal weight:    0.5980
   chunk 63 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 73 optimal weight:    0.7980
   chunk 102 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.7380

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.140309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.103470 restraints weight = 11544.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.105188 restraints weight = 7731.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.106430 restraints weight = 5620.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.106883 restraints weight = 4895.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.107104 restraints weight = 4627.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.4855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8660  Z= 0.114
  Angle     :  0.598   8.934  11740  Z= 0.298
  Chirality :  0.041   0.135   1400
  Planarity :  0.003   0.041   1440
  Dihedral  :  4.913  43.852   1180
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 13.71 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.96 (0.25), residues: 1072
  helix: -0.82 (0.22), residues: 586
  sheet: -0.60 (0.66), residues: 62
  loop : -1.98 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 602 
 TYR   0.008   0.001   TYR A 508 
 PHE   0.011   0.001   PHE A 499 
 TRP   0.009   0.001   TRP A 447 
 HIS   0.004   0.001   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8660)
  covalent geometry    : angle       0.59807 (11740)
  hydrogen bonds       : bond        0.03805 (  336)
  hydrogen bonds       : angle       4.07995 (  978)

*********************** 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
  139 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A  232 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7902 (tp30)
REVERT: A  274 MET cc_start: 0.7692 (mmt) cc_final: 0.7456 (mmt)
REVERT: A  293 ARG cc_start: 0.8068 (ptp-170) cc_final: 0.7824 (ptp-170)
REVERT: A  490 SER cc_start: 0.8819 (m) cc_final: 0.8519 (p)
REVERT: B  232 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7915 (tp30)
REVERT: B  274 MET cc_start: 0.7695 (mmt) cc_final: 0.7449 (mmt)
REVERT: B  420 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8109 (mm)
REVERT: B  514 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8384 (p)
  outliers start: 23
  outliers final: 13
  residues processed: 134
  average time/residue: 0.0962
  time to fit residues: 17.5283
Evaluate side-chains
  113 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  184 SER
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  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 65 optimal weight:    0.0980
   chunk 78 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0570
   chunk 31 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   chunk 96 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    1.0102

-------------------------------------------------------------------------------
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 = 0.3542 r_free = 0.3542 target = 0.140645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.104051 restraints weight = 11425.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.104582 restraints weight = 7631.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.106002 restraints weight = 6178.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.106225 restraints weight = 5171.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.106416 restraints weight = 4931.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.4945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8660  Z= 0.134
  Angle     :  0.658  14.186  11740  Z= 0.313
  Chirality :  0.042   0.189   1400
  Planarity :  0.003   0.040   1440
  Dihedral  :  4.757  42.559   1180
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.01 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.66 (0.26), residues: 1072
  helix: -0.61 (0.22), residues: 594
  sheet: -0.18 (0.70), residues: 62
  loop : -1.86 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 180 
 TYR   0.011   0.001   TYR B 508 
 PHE   0.011   0.001   PHE A 499 
 TRP   0.008   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 8660)
  covalent geometry    : angle       0.65758 (11740)
  hydrogen bonds       : bond        0.03992 (  336)
  hydrogen bonds       : angle       4.01627 (  978)

*********************** 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
  128 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  232 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7869 (tp30)
REVERT: A  274 MET cc_start: 0.7606 (mmt) cc_final: 0.7363 (mmt)
REVERT: A  293 ARG cc_start: 0.8126 (ptp-170) cc_final: 0.7858 (ptp-170)
REVERT: A  490 SER cc_start: 0.8776 (m) cc_final: 0.8448 (p)
REVERT: B  232 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7884 (tp30)
REVERT: B  274 MET cc_start: 0.7691 (mmt) cc_final: 0.7457 (mmt)
REVERT: B  490 SER cc_start: 0.8852 (m) cc_final: 0.8429 (p)
REVERT: B  514 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8344 (p)
  outliers start: 20
  outliers final: 14
  residues processed: 126
  average time/residue: 0.0906
  time to fit residues: 16.0601
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  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
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  479 SER
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  281 LEU
Chi-restraints excluded: chain B residue  337 VAL
Chi-restraints excluded: chain B residue  340 THR
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 63 optimal weight:    0.8980
   chunk 27 optimal weight:   20.0000
   chunk 3 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 75 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3524 r_free = 0.3524 target = 0.139171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.099989 restraints weight = 11722.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.102945 restraints weight = 7534.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.105001 restraints weight = 5734.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.106202 restraints weight = 4800.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 61)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.107203 restraints weight = 4297.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.5065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   8660  Z= 0.174
  Angle     :  0.676  10.900  11740  Z= 0.328
  Chirality :  0.044   0.169   1400
  Planarity :  0.004   0.044   1440
  Dihedral  :  4.851  43.717   1180
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.47 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.47 (0.26), residues: 1072
  helix: -0.43 (0.22), residues: 594
  sheet: -0.13 (0.71), residues: 62
  loop : -1.81 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 602 
 TYR   0.011   0.001   TYR A 508 
 PHE   0.013   0.001   PHE A 499 
 TRP   0.010   0.001   TRP A 447 
 HIS   0.004   0.001   HIS A 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 8660)
  covalent geometry    : angle       0.67646 (11740)
  hydrogen bonds       : bond        0.04489 (  336)
  hydrogen bonds       : angle       4.06249 (  978)

*********************** 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
  137 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A  134 ILE cc_start: 0.6725 (OUTLIER) cc_final: 0.6368 (tt)
REVERT: A  232 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7844 (tp30)
REVERT: A  274 MET cc_start: 0.7605 (mmt) cc_final: 0.7360 (mmt)
REVERT: A  304 PHE cc_start: 0.7515 (m-80) cc_final: 0.7204 (m-80)
REVERT: A  490 SER cc_start: 0.8845 (m) cc_final: 0.8427 (p)
REVERT: B  134 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6409 (tt)
REVERT: B  232 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7846 (tp30)
REVERT: B  274 MET cc_start: 0.7638 (mmt) cc_final: 0.7389 (mmt)
REVERT: B  293 ARG cc_start: 0.8004 (ptp-170) cc_final: 0.7631 (ptp-170)
REVERT: B  490 SER cc_start: 0.8920 (m) cc_final: 0.8406 (p)
REVERT: B  514 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8417 (p)
REVERT: B  569 VAL cc_start: 0.8800 (t) cc_final: 0.8580 (m)
  outliers start: 23
  outliers final: 17
  residues processed: 136
  average time/residue: 0.0906
  time to fit residues: 17.2430
Evaluate side-chains
  125 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  169 LEU
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  479 SER
Chi-restraints excluded: chain A residue  484 HIS
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  162 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  432 ASP
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  514 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 104 optimal weight:    0.0060
   chunk 3 optimal weight:    5.9990
   chunk 40 optimal weight:    0.2980
   chunk 14 optimal weight:    4.9990
   overall best weight:    0.6198

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.147244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.110915 restraints weight = 10992.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.113339 restraints weight = 7895.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.114802 restraints weight = 6368.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.115986 restraints weight = 5525.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.116434 restraints weight = 5055.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.5227

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= 0.102
  Angle     :  0.605  10.865  11740  Z= 0.292
  Chirality :  0.040   0.142   1400
  Planarity :  0.003   0.040   1440
  Dihedral  :  4.576  40.551   1180
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.58 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.01 (0.26), residues: 1072
  helix: -0.09 (0.22), residues: 590
  sheet:  0.11 (0.71), residues: 62
  loop : -1.55 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 602 
 TYR   0.009   0.001   TYR A 508 
 PHE   0.009   0.001   PHE B 499 
 TRP   0.007   0.001   TRP B 447 
 HIS   0.002   0.001   HIS B 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 8660)
  covalent geometry    : angle       0.60534 (11740)
  hydrogen bonds       : bond        0.03301 (  336)
  hydrogen bonds       : angle       3.79821 (  978)

*********************** 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
  135 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  134 ILE cc_start: 0.6951 (OUTLIER) cc_final: 0.6553 (tt)
REVERT: A  274 MET cc_start: 0.7547 (mmt) cc_final: 0.7325 (mmt)
REVERT: A  490 SER cc_start: 0.8722 (m) cc_final: 0.8390 (p)
REVERT: B  134 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6625 (tt)
REVERT: B  293 ARG cc_start: 0.7757 (ptp-170) cc_final: 0.7430 (ptp-170)
REVERT: B  490 SER cc_start: 0.8831 (m) cc_final: 0.8403 (p)
REVERT: B  514 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8290 (p)
  outliers start: 23
  outliers final: 15
  residues processed: 134
  average time/residue: 0.0879
  time to fit residues: 16.5298
Evaluate side-chains
  126 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  169 LEU
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  479 SER
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  162 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  432 ASP
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  514 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 29 optimal weight:    0.7980
   chunk 95 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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
B 461 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.134766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.098132 restraints weight = 11272.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.099835 restraints weight = 8744.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.100819 restraints weight = 7386.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.101834 restraints weight = 6621.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.101834 restraints weight = 6179.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.5278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8660  Z= 0.161
  Angle     :  0.662  11.166  11740  Z= 0.319
  Chirality :  0.043   0.151   1400
  Planarity :  0.003   0.040   1440
  Dihedral  :  4.686  42.703   1180
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 13.82 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.98 (0.26), residues: 1072
  helix: -0.04 (0.22), residues: 594
  sheet:  0.10 (0.70), residues: 62
  loop : -1.57 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 180 
 TYR   0.011   0.001   TYR A 475 
 PHE   0.012   0.001   PHE B 499 
 TRP   0.009   0.001   TRP B 447 
 HIS   0.004   0.001   HIS A 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 8660)
  covalent geometry    : angle       0.66235 (11740)
  hydrogen bonds       : bond        0.04217 (  336)
  hydrogen bonds       : angle       3.91937 (  978)

*********************** 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
  140 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A  134 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6643 (tt)
REVERT: A  211 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7519 (tt0)
REVERT: A  293 ARG cc_start: 0.8024 (ptp-170) cc_final: 0.7574 (ptp-170)
REVERT: A  304 PHE cc_start: 0.7697 (m-80) cc_final: 0.7497 (m-80)
REVERT: A  339 GLN cc_start: 0.7120 (pm20) cc_final: 0.6873 (pm20)
REVERT: A  420 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8346 (mm)
REVERT: A  490 SER cc_start: 0.8728 (m) cc_final: 0.8411 (p)
REVERT: B  134 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6664 (tt)
REVERT: B  211 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7585 (tt0)
REVERT: B  293 ARG cc_start: 0.7894 (ptp-170) cc_final: 0.7529 (ptp-170)
REVERT: B  490 SER cc_start: 0.8861 (m) cc_final: 0.8418 (p)
REVERT: B  514 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8414 (p)
  outliers start: 27
  outliers final: 19
  residues processed: 140
  average time/residue: 0.0918
  time to fit residues: 18.1015
Evaluate side-chains
  133 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  340 THR
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 B residue  128 LEU
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  211 GLU
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  432 ASP
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  514 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 89 optimal weight:    0.2980
   chunk 60 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 50 optimal weight:    0.4980
   chunk 1 optimal weight:    7.9990
   chunk 99 optimal weight:    0.7980
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3543 r_free = 0.3543 target = 0.142965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.107146 restraints weight = 11005.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.109408 restraints weight = 7972.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.110916 restraints weight = 6430.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.111720 restraints weight = 5597.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.112477 restraints weight = 5130.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.5371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8660  Z= 0.140
  Angle     :  0.656  12.019  11740  Z= 0.314
  Chirality :  0.042   0.144   1400
  Planarity :  0.003   0.042   1440
  Dihedral  :  4.665  42.420   1180
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.58 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.87 (0.26), residues: 1072
  helix:  0.01 (0.22), residues: 594
  sheet:  0.22 (0.70), residues: 62
  loop : -1.48 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 602 
 TYR   0.010   0.001   TYR A 475 
 PHE   0.011   0.001   PHE A 499 
 TRP   0.008   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8660)
  covalent geometry    : angle       0.65644 (11740)
  hydrogen bonds       : bond        0.03867 (  336)
  hydrogen bonds       : angle       3.86819 (  978)

********************** 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
  136 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A  134 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6643 (tt)
REVERT: A  211 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7463 (tt0)
REVERT: A  293 ARG cc_start: 0.7912 (ptp-170) cc_final: 0.7486 (ptp-170)
REVERT: A  339 GLN cc_start: 0.7192 (pm20) cc_final: 0.6946 (pm20)
REVERT: A  420 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8452 (mm)
REVERT: A  490 SER cc_start: 0.8716 (m) cc_final: 0.8423 (p)
REVERT: B  134 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6667 (tt)
REVERT: B  211 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7462 (tt0)
REVERT: B  293 ARG cc_start: 0.7767 (ptp-170) cc_final: 0.7427 (ptp-170)
REVERT: B  490 SER cc_start: 0.8784 (m) cc_final: 0.8379 (p)
REVERT: B  514 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8356 (p)
  outliers start: 24
  outliers final: 18
  residues processed: 136
  average time/residue: 0.0932
  time to fit residues: 17.7053
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  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  337 VAL
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 B residue  128 LEU
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  211 GLU
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  432 ASP
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  514 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 61 optimal weight:    0.0980
   chunk 95 optimal weight:    0.7980
   chunk 68 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 77 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 99 optimal weight:    0.4980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3572 r_free = 0.3572 target = 0.143467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.104860 restraints weight = 11451.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.107976 restraints weight = 7314.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.110050 restraints weight = 5511.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.111490 restraints weight = 4599.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.112275 restraints weight = 4077.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.5495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8660  Z= 0.100
  Angle     :  0.619  11.290  11740  Z= 0.294
  Chirality :  0.040   0.149   1400
  Planarity :  0.003   0.043   1440
  Dihedral  :  4.452  39.802   1180
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 14.79 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.51 (0.27), residues: 1072
  helix:  0.31 (0.22), residues: 592
  sheet:  0.57 (0.71), residues: 62
  loop : -1.37 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 602 
 TYR   0.012   0.001   TYR A 475 
 PHE   0.008   0.001   PHE B 499 
 TRP   0.007   0.001   TRP B 447 
 HIS   0.002   0.001   HIS B 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 8660)
  covalent geometry    : angle       0.61913 (11740)
  hydrogen bonds       : bond        0.03140 (  336)
  hydrogen bonds       : angle       3.71479 (  978)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1410.50 seconds
wall clock time: 25 minutes 2.06 seconds (1502.06 seconds total)