Starting phenix.real_space_refine
on Sun Aug 24 02:15:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qtz_18655/08_2025/8qtz_18655.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qtz_18655/08_2025/8qtz_18655.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qtz_18655/08_2025/8qtz_18655.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qtz_18655/08_2025/8qtz_18655.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qtz_18655/08_2025/8qtz_18655.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qtz_18655/08_2025/8qtz_18655.map"
  }
  resolution = 4.27
  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=   0.088 sd=   0.830
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   10258      2.51       5
     N    2726      2.21       5
     O    3224      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16260
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "X"
      Number of atoms: 5977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 760, 5977
          Classifications: {'peptide': 760}
          Link IDs: {'PTRANS': 34, 'TRANS': 725}
          Chain breaks: 1
    Chain: "Y"
      Number of atoms: 5977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 760, 5977
          Classifications: {'peptide': 760}
          Link IDs: {'PTRANS': 34, 'TRANS': 725}
          Chain breaks: 1
    Chain: "Z"
      Number of atoms: 4306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 547, 4306
          Classifications: {'peptide': 547}
          Link IDs: {'PTRANS': 17, 'TRANS': 529}
          Chain breaks: 1
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   GLY X 156 " occ=0.96
      ... (2 atoms not shown)
      pdb=" O   GLY X 156 " occ=0.96
  Time building chain proxies: 3.45, per 1000 atoms: 0.21
  Number of scatterers: 16260
  At special positions: 0
  Unit cell: (175.89, 175.89, 154.44, 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    3224      8.00
     N    2726      7.00
     C   10258      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.34
  Conformation dependent library (CDL) restraints added in 658.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3922

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 27 sheets defined
      30.1% alpha, 15.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'X' and resid 1 through 12
    Processing helix  chain 'X' and resid 15 through 26
    Processing helix  chain 'X' and resid 212 through 222
      removed outlier: 3.662A  pdb=" N   CYS X 216 " --> pdb=" O   GLU X 212 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 359 through 365
    Processing helix  chain 'X' and resid 494 through 510
      removed outlier: 4.053A  pdb=" N   LEU X 498 " --> pdb=" O   LEU X 494 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLU X 500 " --> pdb=" O   ARG X 496 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   GLU X 503 " --> pdb=" O   GLY X 499 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   GLU X 504 " --> pdb=" O   GLU X 500 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 515 through 523
      removed outlier: 3.724A  pdb=" N   ASP X 519 " --> pdb=" O   SER X 515 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU X 522 " --> pdb=" O   ILE X 518 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU X 523 " --> pdb=" O   ASP X 519 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 526 through 533
      removed outlier: 3.728A  pdb=" N   PHE X 531 " --> pdb=" O   MET X 527 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   GLY X 533 " --> pdb=" O   SER X 529 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 543 through 553
    Processing helix  chain 'X' and resid 555 through 572
      removed outlier: 3.638A  pdb=" N   ASN X 559 " --> pdb=" O   SER X 555 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 594 through 598
      removed outlier: 3.643A  pdb=" N   GLN X 597 " --> pdb=" O   VAL X 594 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE X 598 " --> pdb=" O   SER X 595 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'X' and resid 594 through 598'
    Processing helix  chain 'X' and resid 606 through 624
      removed outlier: 3.996A  pdb=" N   THR X 610 " --> pdb=" O   SER X 606 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLN X 611 " --> pdb=" O   SER X 607 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ARG X 618 " --> pdb=" O   THR X 614 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 632 through 646
      removed outlier: 3.816A  pdb=" N   ILE X 636 " --> pdb=" O   ASN X 632 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 655 through 667
      removed outlier: 3.928A  pdb=" N   ILE X 659 " --> pdb=" O   THR X 655 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 704 through 713
      removed outlier: 3.529A  pdb=" N   LEU X 711 " --> pdb=" O   LYS X 707 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 723 through 731
    Processing helix  chain 'X' and resid 739 through 744
    Processing helix  chain 'X' and resid 748 through 759
      removed outlier: 4.184A  pdb=" N   LEU X 752 " --> pdb=" O   ASP X 748 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLN X 758 " --> pdb=" O   GLU X 754 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 761 through 774
      removed outlier: 3.869A  pdb=" N   ASN X 765 " --> pdb=" O   PRO X 761 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 2 through 12
    Processing helix  chain 'Y' and resid 12 through 29
      removed outlier: 3.861A  pdb=" N   ASP Y  17 " --> pdb=" O   SER Y  13 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   LEU Y  18 " --> pdb=" O   TYR Y  14 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 120 through 124
    Processing helix  chain 'Y' and resid 209 through 211
      No H-bonds generated for 'chain 'Y' and resid 209 through 211'
    Processing helix  chain 'Y' and resid 212 through 222
    Processing helix  chain 'Y' and resid 359 through 364
      removed outlier: 3.514A  pdb=" N   ASN Y 364 " --> pdb=" O   GLN Y 360 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 497 through 510
      removed outlier: 3.842A  pdb=" N   LEU Y 501 " --> pdb=" O   GLN Y 497 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 514 through 521
    Processing helix  chain 'Y' and resid 528 through 532
    Processing helix  chain 'Y' and resid 540 through 553
      removed outlier: 4.000A  pdb=" N   LYS Y 553 " --> pdb=" O   MET Y 549 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 555 through 574
      removed outlier: 3.821A  pdb=" N   SER Y 574 " --> pdb=" O   ASP Y 570 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 592 through 597
      removed outlier: 3.535A  pdb=" N   THR Y 596 " --> pdb=" O   THR Y 592 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 608 through 619
    Processing helix  chain 'Y' and resid 620 through 625
    Processing helix  chain 'Y' and resid 632 through 647
      removed outlier: 3.816A  pdb=" N   ILE Y 636 " --> pdb=" O   ASN Y 632 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   ALA Y 639 " --> pdb=" O   ASP Y 635 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   LYS Y 647 " --> pdb=" O   THR Y 643 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 652 through 654
      No H-bonds generated for 'chain 'Y' and resid 652 through 654'
    Processing helix  chain 'Y' and resid 655 through 667
      removed outlier: 4.060A  pdb=" N   ILE Y 659 " --> pdb=" O   THR Y 655 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   THR Y 661 " --> pdb=" O   PRO Y 657 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 705 through 713
      removed outlier: 3.799A  pdb=" N   THR Y 713 " --> pdb=" O   ALA Y 709 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 723 through 734
    Processing helix  chain 'Y' and resid 737 through 745
    Processing helix  chain 'Y' and resid 748 through 758
      removed outlier: 4.023A  pdb=" N   LEU Y 752 " --> pdb=" O   ASP Y 748 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   GLN Y 758 " --> pdb=" O   GLU Y 754 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 762 through 774
    Processing helix  chain 'Z' and resid 2 through 12
    Processing helix  chain 'Z' and resid 15 through 26
      removed outlier: 3.677A  pdb=" N   SER Z  19 " --> pdb=" O   THR Z  15 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 359 through 364
      removed outlier: 3.593A  pdb=" N   ARG Z 363 " --> pdb=" O   SER Z 359 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 502 through 511
    Processing helix  chain 'Z' and resid 515 through 521
      removed outlier: 3.504A  pdb=" N   ASP Z 519 " --> pdb=" O   SER Z 515 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 526 through 531
      removed outlier: 3.542A  pdb=" N   PHE Z 531 " --> pdb=" O   MET Z 527 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 540 through 552
      removed outlier: 4.622A  pdb=" N   MET Z 549 " --> pdb=" O   ALA Z 545 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 553 through 555
      No H-bonds generated for 'chain 'Z' and resid 553 through 555'
    Processing helix  chain 'Z' and resid 557 through 571
    Processing helix  chain 'Z' and resid 607 through 624
      removed outlier: 3.652A  pdb=" N   GLN Z 611 " --> pdb=" O   SER Z 607 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   MET Z 624 " --> pdb=" O   ARG Z 620 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 632 through 647
      removed outlier: 3.903A  pdb=" N   ILE Z 636 " --> pdb=" O   ASN Z 632 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 655 through 667
      removed outlier: 4.860A  pdb=" N   THR Z 661 " --> pdb=" O   PRO Z 657 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 705 through 714
      removed outlier: 4.149A  pdb=" N   ASP Z 714 " --> pdb=" O   ASP Z 710 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 723 through 735
    Processing helix  chain 'Z' and resid 737 through 746
    Processing helix  chain 'Z' and resid 748 through 759
      removed outlier: 3.535A  pdb=" N   LEU Z 752 " --> pdb=" O   ASP Z 748 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLN Z 758 " --> pdb=" O   GLU Z 754 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   ASP Z 759 " --> pdb=" O   PHE Z 755 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 761 through 774
      removed outlier: 3.663A  pdb=" N   ASN Z 765 " --> pdb=" O   PRO Z 761 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   CYS Z 774 " --> pdb=" O   LEU Z 770 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'X' and resid 49 through 50
  WARNING: can't find start of bonding for strands!
    previous: chain 'X' and resid 49 through 50
    current: chain 'X' and resid 402 through 415
      removed outlier: 4.999A  pdb=" N   ARG X 427 " --> pdb=" O   ALA X 407 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   VAL X 409 " --> pdb=" O   ARG X 425 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   ARG X 425 " --> pdb=" O   VAL X 409 " (cutoff:3.500A)
      removed outlier: 5.281A  pdb=" N   LEU X 411 " --> pdb=" O   SER X 423 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   SER X 423 " --> pdb=" O   LEU X 411 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   THR X 413 " --> pdb=" O   LEU X 421 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   LEU X 421 " --> pdb=" O   THR X 413 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'X' and resid 420 through 432
    current: chain 'Y' and resid 310 through 315
  WARNING: can't find start of bonding for strands!
    previous: chain 'Y' and resid 310 through 315
    current: chain 'Y' and resid 350 through 357
  WARNING: can't find start of bonding for strands!
    previous: chain 'Y' and resid 350 through 357
    current: chain 'Y' and resid 401 through 416
      removed outlier: 5.146A  pdb=" N   LEU Y 404 " --> pdb=" O   ALA Y 431 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ALA Y 431 " --> pdb=" O   LEU Y 404 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   SER Y 406 " --> pdb=" O   ARG Y 429 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ARG Y 429 " --> pdb=" O   SER Y 406 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   GLY Y 408 " --> pdb=" O   ARG Y 427 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'X' and resid 60 through 61
      removed outlier: 6.163A  pdb=" N   THR X  60 " --> pdb=" O   ASP Y 325 " (cutoff:3.500A)
      removed outlier: 8.426A  pdb=" N   SER Y 327 " --> pdb=" O   THR X  60 " (cutoff:3.500A)
      removed outlier: 5.778A  pdb=" N   PHE Y 328 " --> pdb=" O   SER Y 340 " (cutoff:3.500A)
      removed outlier: 5.226A  pdb=" N   SER Y 340 " --> pdb=" O   PHE Y 328 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   GLY Y 330 " --> pdb=" O   VAL Y 338 " (cutoff:3.500A)
      removed outlier: 5.234A  pdb=" N   VAL Y 338 " --> pdb=" O   GLY Y 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'X' and resid 73 through 74
      removed outlier: 4.644A  pdb=" N   VAL X  93 " --> pdb=" O   THR X 105 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   THR X 105 " --> pdb=" O   VAL X  93 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'X' and resid 80 through 83
      removed outlier: 3.555A  pdb=" N   TYR X 206 " --> pdb=" O   LEU X  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'X' and resid 116 through 121
      removed outlier: 4.125A  pdb=" N   ARG X 117 " --> pdb=" O   LEU X 128 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   LEU X 128 " --> pdb=" O   ARG X 117 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'X' and resid 138 through 140
      removed outlier: 3.641A  pdb=" N   TRP X 138 " --> pdb=" O   SER X 160 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'X' and resid 252 through 267
  WARNING: can't find start of bonding for strands!
    previous: chain 'X' and resid 252 through 267
    current: chain 'X' and resid 469 through 474
  WARNING: can't find start of bonding for strands!
    previous: chain 'X' and resid 469 through 474
    current: chain 'Y' and resid 462 through 474
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'X' and resid 270 through 275
    Processing sheet with id=AA9, first strand: chain 'X' and resid 279 through 282
      removed outlier: 9.066A  pdb=" N   TRP X 291 " --> pdb=" O   SER X 340 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   PHE X 342 " --> pdb=" O   TRP X 291 " (cutoff:3.500A)
      removed outlier: 8.762A  pdb=" N   GLU X 293 " --> pdb=" O   PHE X 342 " (cutoff:3.500A)
      removed outlier: 11.261A  pdb=" N   VAL X 344 " --> pdb=" O   GLU X 293 " (cutoff:3.500A)
      removed outlier: 10.414A  pdb=" N   SER X 295 " --> pdb=" O   VAL X 344 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'X' and resid 315 through 317
      removed outlier: 3.924A  pdb=" N   THR X 317 " --> pdb=" O   ASP X 354 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'X' and resid 320 through 321
    Processing sheet with id=AB3, first strand: chain 'X' and resid 384 through 386
    Processing sheet with id=AB4, first strand: chain 'X' and resid 693 through 694
      removed outlier: 3.750A  pdb=" N   TYR X 693 " --> pdb=" O   VAL X 681 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL X 681 " --> pdb=" O   TYR X 693 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   VAL X 675 " --> pdb=" O   PHE X 682 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'Y' and resid 33 through 34
  WARNING: can't find start of bonding for strands!
    previous: chain 'Y' and resid 33 through 34
    current: chain 'Z' and resid 290 through 295
  WARNING: can't find start of bonding for strands!
    previous: chain 'Z' and resid 290 through 295
    current: chain 'Z' and resid 338 through 345
    Processing sheet with id=AB6, first strand: chain 'Y' and resid 81 through 82
    Processing sheet with id=AB7, first strand: chain 'Y' and resid 95 through 96
      removed outlier: 3.932A  pdb=" N   TRP Y 102 " --> pdb=" O   LYS Y 145 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA Y 104 " --> pdb=" O   VAL Y 143 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   TRP Y 138 " --> pdb=" O   LEU Y 159 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   LEU Y 159 " --> pdb=" O   TRP Y 138 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   PHE Y 140 " --> pdb=" O   SER Y 157 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'Y' and resid 115 through 116
      removed outlier: 3.554A  pdb=" N   VAL Y 130 " --> pdb=" O   GLU Y 115 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'Y' and resid 177 through 178
    Processing sheet with id=AC1, first strand: chain 'Y' and resid 278 through 281
      removed outlier: 4.010A  pdb=" N   ALA Y 278 " --> pdb=" O   LYS Y 297 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   THR Y 280 " --> pdb=" O   SER Y 295 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'Y' and resid 384 through 386
    Processing sheet with id=AC3, first strand: chain 'Y' and resid 680 through 685
    Processing sheet with id=AC4, first strand: chain 'Z' and resid 263 through 264
      removed outlier: 3.573A  pdb=" N   LYS Z 263 " --> pdb=" O   VAL Z 474 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'Z' and resid 271 through 273
    Processing sheet with id=AC6, first strand: chain 'Z' and resid 300 through 307
      removed outlier: 3.616A  pdb=" N   TYR Z 303 " --> pdb=" O   ALA Z 314 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   THR Z 317 " --> pdb=" O   ASP Z 354 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ASP Z 354 " --> pdb=" O   THR Z 317 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   VAL Z 351 " --> pdb=" O   PHE Z 428 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   PHE Z 428 " --> pdb=" O   VAL Z 351 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   LEU Z 421 " --> pdb=" O   THR Z 413 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   THR Z 413 " --> pdb=" O   LEU Z 421 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   SER Z 423 " --> pdb=" O   LEU Z 411 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   LEU Z 411 " --> pdb=" O   SER Z 423 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   ARG Z 425 " --> pdb=" O   VAL Z 409 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   VAL Z 409 " --> pdb=" O   ARG Z 425 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   ARG Z 427 " --> pdb=" O   ALA Z 407 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   CYS Z 380 " --> pdb=" O   VAL Z 402 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'Z' and resid 371 through 372
      removed outlier: 3.768A  pdb=" N   ALA Z 372 " --> pdb=" O   SER Z 469 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'Z' and resid 384 through 386
    Processing sheet with id=AC9, first strand: chain 'Z' and resid 690 through 694
      removed outlier: 3.867A  pdb=" N   PHE Z 682 " --> pdb=" O   VAL Z 675 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   VAL Z 675 " --> pdb=" O   PHE Z 682 " (cutoff:3.500A)

    473 hydrogen bonds defined for protein.
    1332 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.31

  Time building geometry restraints manager: 1.75 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: 5251
        1.34 -     1.46: 2833
        1.46 -     1.58: 8406
        1.58 -     1.70: 0
        1.70 -     1.81: 91
  Bond restraints: 16581
  Sorted by residual:
  bond pdb=" N   ASP Y 658 "
       pdb=" CA  ASP Y 658 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.038 1.29e-02 6.01e+03 8.88e+00
  bond pdb=" N   ALA X 541 "
       pdb=" CA  ALA X 541 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.032 1.29e-02 6.01e+03 6.25e+00
  bond pdb=" N   SER X 543 "
       pdb=" CA  SER X 543 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.29e-02 6.01e+03 6.13e+00
  bond pdb=" N   SER Y   3 "
       pdb=" CA  SER Y   3 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.29e-02 6.01e+03 6.12e+00
  bond pdb=" N   ILE Y 656 "
       pdb=" CA  ILE Y 656 "
    ideal  model  delta    sigma   weight residual
    1.464  1.495 -0.030 1.23e-02 6.61e+03 6.12e+00
  ... (remaining 16576 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.22: 21890
        2.22 -     4.44: 517
        4.44 -     6.66: 98
        6.66 -     8.88: 13
        8.88 -    11.10: 5
  Bond angle restraints: 22523
  Sorted by residual:
  angle pdb=" C   ASN Y  97 "
        pdb=" N   ASN Y  98 "
        pdb=" CA  ASN Y  98 "
      ideal   model   delta    sigma   weight residual
     121.54  132.24  -10.70 1.91e+00 2.74e-01 3.14e+01
  angle pdb=" C   ASN X  97 "
        pdb=" N   ASN X  98 "
        pdb=" CA  ASN X  98 "
      ideal   model   delta    sigma   weight residual
     121.54  131.66  -10.12 1.91e+00 2.74e-01 2.81e+01
  angle pdb=" N   VAL X 366 "
        pdb=" CA  VAL X 366 "
        pdb=" C   VAL X 366 "
      ideal   model   delta    sigma   weight residual
     112.12  108.02    4.10 8.40e-01 1.42e+00 2.38e+01
  angle pdb=" C   GLN Z 393 "
        pdb=" N   TRP Z 394 "
        pdb=" CA  TRP Z 394 "
      ideal   model   delta    sigma   weight residual
     120.68  128.03   -7.35 1.52e+00 4.33e-01 2.34e+01
  angle pdb=" CA  PRO Y 657 "
        pdb=" C   PRO Y 657 "
        pdb=" O   PRO Y 657 "
      ideal   model   delta    sigma   weight residual
     121.34  116.13    5.21 1.14e+00 7.69e-01 2.09e+01
  ... (remaining 22518 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.23: 8989
       17.23 -    34.46: 829
       34.46 -    51.68: 141
       51.68 -    68.91: 23
       68.91 -    86.14: 17
  Dihedral angle restraints: 9999
    sinusoidal: 3935
      harmonic: 6064
  Sorted by residual:
  dihedral pdb=" CA  ARG Y 210 "
           pdb=" C   ARG Y 210 "
           pdb=" N   SER Y 211 "
           pdb=" CA  SER Y 211 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.15  -28.85     0      5.00e+00 4.00e-02 3.33e+01
  dihedral pdb=" CA  MET Z 549 "
           pdb=" C   MET Z 549 "
           pdb=" N   LYS Z 550 "
           pdb=" CA  LYS Z 550 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.53   25.47     0      5.00e+00 4.00e-02 2.60e+01
  dihedral pdb=" C   ASP Y 658 "
           pdb=" N   ASP Y 658 "
           pdb=" CA  ASP Y 658 "
           pdb=" CB  ASP Y 658 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.25   12.65     0      2.50e+00 1.60e-01 2.56e+01
  ... (remaining 9996 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 2348
       0.086 -    0.172: 216
       0.172 -    0.258: 8
       0.258 -    0.343: 3
       0.343 -    0.429: 2
  Chirality restraints: 2577
  Sorted by residual:
  chirality pdb=" CA  ASP Y 658 "
            pdb=" N   ASP Y 658 "
            pdb=" C   ASP Y 658 "
            pdb=" CB  ASP Y 658 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.61e+00
  chirality pdb=" CB  ILE Z 668 "
            pdb=" CA  ILE Z 668 "
            pdb=" CG1 ILE Z 668 "
            pdb=" CG2 ILE Z 668 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.23    0.41 2.00e-01 2.50e+01 4.23e+00
  chirality pdb=" CB  ILE X  55 "
            pdb=" CA  ILE X  55 "
            pdb=" CG1 ILE X  55 "
            pdb=" CG2 ILE X  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.83e+00
  ... (remaining 2574 not shown)

  Planarity restraints: 2917
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP X 356 "    0.010 2.00e-02 2.50e+03   1.79e-02 7.99e+00
        pdb=" CG  TRP X 356 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TRP X 356 "    0.029 2.00e-02 2.50e+03
        pdb=" CD2 TRP X 356 "    0.011 2.00e-02 2.50e+03
        pdb=" NE1 TRP X 356 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP X 356 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE3 TRP X 356 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ2 TRP X 356 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ3 TRP X 356 "    0.011 2.00e-02 2.50e+03
        pdb=" CH2 TRP X 356 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP Y 454 "   -0.045 5.00e-02 4.00e+02   6.75e-02 7.30e+00
        pdb=" N   PRO Y 455 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO Y 455 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO Y 455 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU Y 224 "    0.037 5.00e-02 4.00e+02   5.68e-02 5.17e+00
        pdb=" N   PRO Y 225 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO Y 225 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO Y 225 "    0.031 5.00e-02 4.00e+02
  ... (remaining 2914 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 409
        2.63 -     3.20: 16486
        3.20 -     3.77: 25866
        3.77 -     4.33: 34000
        4.33 -     4.90: 52553
  Nonbonded interactions: 129314
  Sorted by model distance:
  nonbonded pdb=" OG  SER X 257 "
            pdb=" OE2 GLU Y 264 "
     model   vdw
     2.065 3.040
  nonbonded pdb=" OG  SER Y 583 "
            pdb=" OE1 GLN Y 597 "
     model   vdw
     2.099 3.040
  nonbonded pdb=" OG  SER Y 160 "
            pdb=" OH  TYR Y 165 "
     model   vdw
     2.128 3.040
  nonbonded pdb=" OG  SER Y 586 "
            pdb=" OE1 GLN Y 706 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" O   SER Z 292 "
            pdb=" OG  SER Z 340 "
     model   vdw
     2.151 3.040
  ... (remaining 129309 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'X'
  selection = chain 'Y'
}

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=0.00 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:             0.590
  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:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.310
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
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      :  0.004   0.046  16581  Z= 0.187
  Angle     :  0.863  11.101  22523  Z= 0.479
  Chirality :  0.050   0.429   2577
  Planarity :  0.005   0.068   2917
  Dihedral  : 13.806  86.141   6077
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 21.72
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 11.00 %
    Favored  : 88.66 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.38 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.05 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.58 (0.17), residues: 2055
  helix: -1.04 (0.21), residues: 525
  sheet: -1.74 (0.23), residues: 483
  loop : -3.52 (0.17), residues: 1047

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG Y 446 
 TYR   0.026   0.002   TYR X 219 
 PHE   0.029   0.002   PHE Y 505 
 TRP   0.038   0.003   TRP X 356 
 HIS   0.002   0.001   HIS Y 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (16581)
  covalent geometry    : angle       0.86314 (22523)
  hydrogen bonds       : bond        0.21086 (  473)
  hydrogen bonds       : angle       8.65012 ( 1332)

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

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

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  611 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 610
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   23 GLN cc_start: 0.8818 (mm110) cc_final: 0.8506 (tp-100)
REVERT: X   25 ILE cc_start: 0.9111 (tp) cc_final: 0.8799 (tp)
REVERT: X   31 GLN cc_start: 0.7421 (tm-30) cc_final: 0.6607 (tm-30)
REVERT: X   33 VAL cc_start: 0.7539 (t) cc_final: 0.6929 (p)
REVERT: X   81 TRP cc_start: 0.6931 (m100) cc_final: 0.5851 (m100)
REVERT: X  140 PHE cc_start: 0.7319 (t80) cc_final: 0.6985 (t80)
REVERT: X  224 LEU cc_start: 0.8331 (tt) cc_final: 0.7992 (tt)
REVERT: X  263 LYS cc_start: 0.8088 (tptt) cc_final: 0.7642 (ttmt)
REVERT: X  321 ASN cc_start: 0.8145 (t0) cc_final: 0.7732 (t0)
REVERT: X  367 TYR cc_start: 0.8138 (m-80) cc_final: 0.7643 (m-80)
REVERT: X  375 LEU cc_start: 0.8945 (mm) cc_final: 0.8683 (mt)
REVERT: X  512 ILE cc_start: 0.9218 (mm) cc_final: 0.8924 (mm)
REVERT: X  575 ILE cc_start: 0.9369 (mm) cc_final: 0.8970 (mp)
REVERT: X  634 ASP cc_start: 0.8670 (m-30) cc_final: 0.8461 (m-30)
REVERT: X  687 ASP cc_start: 0.8218 (m-30) cc_final: 0.8016 (t0)
REVERT: X  699 GLU cc_start: 0.8338 (mp0) cc_final: 0.7457 (mp0)
REVERT: X  710 ASP cc_start: 0.8215 (p0) cc_final: 0.7847 (m-30)
REVERT: X  718 ILE cc_start: 0.8856 (tp) cc_final: 0.8526 (tp)
REVERT: X  729 ASN cc_start: 0.9071 (t0) cc_final: 0.8832 (t0)
REVERT: X  770 LEU cc_start: 0.9079 (tt) cc_final: 0.8702 (tp)
REVERT: X  773 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8064 (tm-30)
REVERT: Y  258 LYS cc_start: 0.9131 (mmmt) cc_final: 0.8869 (mmmm)
REVERT: Y  271 ILE cc_start: 0.8830 (mm) cc_final: 0.8011 (mm)
REVERT: Y  273 ILE cc_start: 0.8635 (tp) cc_final: 0.8292 (tp)
REVERT: Y  328 PHE cc_start: 0.8680 (t80) cc_final: 0.8413 (t80)
REVERT: Y  367 TYR cc_start: 0.8547 (m-80) cc_final: 0.8221 (m-80)
REVERT: Y  460 GLU cc_start: 0.7938 (tp30) cc_final: 0.7734 (tp30)
REVERT: Y  530 MET cc_start: 0.8873 (tpt) cc_final: 0.8587 (tpp)
REVERT: Y  549 MET cc_start: 0.7879 (mtm) cc_final: 0.7532 (mmm)
REVERT: Y  596 THR cc_start: 0.8620 (p) cc_final: 0.8404 (p)
REVERT: Y  634 ASP cc_start: 0.7797 (p0) cc_final: 0.7050 (p0)
REVERT: Y  643 THR cc_start: 0.9302 (m) cc_final: 0.8955 (t)
REVERT: Y  645 ILE cc_start: 0.8878 (pt) cc_final: 0.8656 (pt)
REVERT: Y  662 GLU cc_start: 0.8849 (pt0) cc_final: 0.8516 (pt0)
REVERT: Y  673 TYR cc_start: 0.7905 (m-80) cc_final: 0.7602 (m-80)
REVERT: Y  727 LEU cc_start: 0.9095 (mt) cc_final: 0.8877 (mt)
REVERT: Y  743 ASN cc_start: 0.8984 (m-40) cc_final: 0.8667 (m-40)
REVERT: Y  744 LEU cc_start: 0.9428 (mm) cc_final: 0.9048 (mm)
REVERT: Y  753 ARG cc_start: 0.8065 (mtp-110) cc_final: 0.7769 (ttt90)
REVERT: Y  765 ASN cc_start: 0.8319 (t0) cc_final: 0.8067 (t0)
REVERT: Y  769 GLN cc_start: 0.7318 (mm110) cc_final: 0.6701 (mm110)
REVERT: Y  773 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8440 (tm-30)
REVERT: Z    1 MET cc_start: 0.8723 (tmm) cc_final: 0.8367 (tmm)
REVERT: Z  271 ILE cc_start: 0.9287 (tp) cc_final: 0.8685 (tp)
REVERT: Z  352 TYR cc_start: 0.8005 (m-10) cc_final: 0.7727 (m-80)
REVERT: Z  422 ASN cc_start: 0.8304 (p0) cc_final: 0.8015 (p0)
REVERT: Z  494 LEU cc_start: 0.8489 (mp) cc_final: 0.8190 (tt)
REVERT: Z  505 PHE cc_start: 0.8186 (m-80) cc_final: 0.7528 (m-80)
REVERT: Z  525 LEU cc_start: 0.8748 (pt) cc_final: 0.8428 (pp)
REVERT: Z  611 GLN cc_start: 0.8767 (mp10) cc_final: 0.8395 (mp10)
REVERT: Z  631 MET cc_start: 0.8215 (tmm) cc_final: 0.7863 (tmm)
REVERT: Z  632 ASN cc_start: 0.8299 (t0) cc_final: 0.7503 (p0)
REVERT: Z  643 THR cc_start: 0.8446 (p) cc_final: 0.8147 (p)
REVERT: Z  644 LYS cc_start: 0.8507 (mmtp) cc_final: 0.8234 (mttm)
REVERT: Z  659 ILE cc_start: 0.8907 (mm) cc_final: 0.8644 (tp)
REVERT: Z  666 LYS cc_start: 0.8799 (mmmm) cc_final: 0.8512 (mmmm)
REVERT: Z  676 ILE cc_start: 0.8888 (mm) cc_final: 0.8617 (tp)
REVERT: Z  682 PHE cc_start: 0.7559 (p90) cc_final: 0.7023 (p90)
REVERT: Z  683 GLU cc_start: 0.7692 (pp20) cc_final: 0.7399 (pm20)
REVERT: Z  714 ASP cc_start: 0.8386 (t0) cc_final: 0.8056 (t0)
REVERT: Z  721 ILE cc_start: 0.9135 (mt) cc_final: 0.8457 (mt)
REVERT: Z  728 LYS cc_start: 0.6037 (ttpt) cc_final: 0.5787 (tppt)
REVERT: Z  739 GLN cc_start: 0.8097 (tp-100) cc_final: 0.6794 (tp40)
REVERT: Z  748 ASP cc_start: 0.8928 (t0) cc_final: 0.8708 (t0)
REVERT: Z  754 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8397 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 610
  average time/residue: 0.1201
  time to fit residues: 107.1915
Evaluate side-chains
  494 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 494
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 98 optimal weight:    0.0000
   chunk 194 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    9.9990
   chunk 200 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    5.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** X 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 559 ASN
X 757 ASN
** Y  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 228 GLN
** Y 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 678 ASN
Y 731 ASN
** Z 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z 773 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.079171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.066940 restraints weight = 65011.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.068992 restraints weight = 35661.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.070367 restraints weight = 22413.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.071326 restraints weight = 15402.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.071966 restraints weight = 11356.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  16581  Z= 0.164
  Angle     :  0.761   9.482  22523  Z= 0.395
  Chirality :  0.048   0.249   2577
  Planarity :  0.005   0.060   2917
  Dihedral  :  5.887  26.253   2239
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 17.53
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 11.34 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  6.10 %
    Favored  : 93.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.62 (0.17), residues: 2055
  helix: -1.15 (0.20), residues: 548
  sheet: -1.66 (0.24), residues: 447
  loop : -3.56 (0.16), residues: 1060

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG Z 369 
 TYR   0.024   0.002   TYR X 461 
 PHE   0.039   0.002   PHE X 505 
 TRP   0.026   0.002   TRP X 356 
 HIS   0.002   0.001   HIS Y 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (16581)
  covalent geometry    : angle       0.76071 (22523)
  hydrogen bonds       : bond        0.05152 (  473)
  hydrogen bonds       : angle       6.72806 ( 1332)

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

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

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  541 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 531
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X    1 MET cc_start: 0.6068 (tpt) cc_final: 0.5621 (tpt)
REVERT: X   20 ASP cc_start: 0.8811 (p0) cc_final: 0.8572 (p0)
REVERT: X   23 GLN cc_start: 0.8859 (mm110) cc_final: 0.8594 (tp-100)
REVERT: X   81 TRP cc_start: 0.7289 (m100) cc_final: 0.6027 (m100)
REVERT: X  263 LYS cc_start: 0.8299 (tptt) cc_final: 0.7822 (ttmt)
REVERT: X  367 TYR cc_start: 0.8343 (m-80) cc_final: 0.7710 (m-80)
REVERT: X  423 SER cc_start: 0.9182 (t) cc_final: 0.8888 (p)
REVERT: X  425 ARG cc_start: 0.8313 (tpp-160) cc_final: 0.7949 (mmt180)
REVERT: X  512 ILE cc_start: 0.9134 (mm) cc_final: 0.8861 (mm)
REVERT: X  530 MET cc_start: 0.8634 (ttp) cc_final: 0.8419 (ttp)
REVERT: X  531 PHE cc_start: 0.9116 (m-10) cc_final: 0.8803 (m-80)
REVERT: X  551 LYS cc_start: 0.9146 (ttmt) cc_final: 0.8795 (ttpt)
REVERT: X  575 ILE cc_start: 0.9315 (mm) cc_final: 0.8997 (mp)
REVERT: X  624 MET cc_start: 0.7572 (mtp) cc_final: 0.7155 (mtm)
REVERT: X  631 MET cc_start: 0.8504 (tpp) cc_final: 0.8134 (tpp)
REVERT: X  635 ASP cc_start: 0.8963 (m-30) cc_final: 0.8492 (m-30)
REVERT: X  662 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8026 (pt0)
REVERT: X  666 LYS cc_start: 0.9221 (mtmm) cc_final: 0.8869 (mtmm)
REVERT: X  687 ASP cc_start: 0.8480 (m-30) cc_final: 0.7955 (t0)
REVERT: X  694 LYS cc_start: 0.8661 (tptp) cc_final: 0.8310 (tptt)
REVERT: X  699 GLU cc_start: 0.7808 (mp0) cc_final: 0.7514 (mp0)
REVERT: X  707 LYS cc_start: 0.8719 (tptp) cc_final: 0.8250 (tptp)
REVERT: X  718 ILE cc_start: 0.8988 (tp) cc_final: 0.8513 (tp)
REVERT: X  729 ASN cc_start: 0.9125 (t0) cc_final: 0.8910 (t0)
REVERT: X  762 ILE cc_start: 0.8420 (pt) cc_final: 0.8103 (pt)
REVERT: X  773 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8187 (tm-30)
REVERT: Y   17 ASP cc_start: 0.8719 (p0) cc_final: 0.8145 (p0)
REVERT: Y  107 LEU cc_start: 0.8708 (tp) cc_final: 0.7804 (tp)
REVERT: Y  271 ILE cc_start: 0.8795 (mm) cc_final: 0.8152 (mm)
REVERT: Y  328 PHE cc_start: 0.8472 (t80) cc_final: 0.8237 (t80)
REVERT: Y  337 PHE cc_start: 0.7871 (m-80) cc_final: 0.7438 (m-80)
REVERT: Y  352 TYR cc_start: 0.8714 (m-80) cc_final: 0.8360 (m-10)
REVERT: Y  415 PHE cc_start: 0.7732 (t80) cc_final: 0.7063 (t80)
REVERT: Y  527 MET cc_start: 0.8491 (ppp) cc_final: 0.8144 (ppp)
REVERT: Y  539 ASP cc_start: 0.7668 (t70) cc_final: 0.7370 (t0)
REVERT: Y  549 MET cc_start: 0.7814 (mtm) cc_final: 0.7609 (mmm)
REVERT: Y  566 ASP cc_start: 0.8252 (p0) cc_final: 0.8012 (p0)
REVERT: Y  619 LEU cc_start: 0.8631 (mm) cc_final: 0.7970 (tp)
REVERT: Y  634 ASP cc_start: 0.8040 (p0) cc_final: 0.7303 (p0)
REVERT: Y  643 THR cc_start: 0.9275 (m) cc_final: 0.9007 (t)
REVERT: Y  645 ILE cc_start: 0.8954 (pt) cc_final: 0.8719 (pt)
REVERT: Y  662 GLU cc_start: 0.8878 (pt0) cc_final: 0.8498 (pt0)
REVERT: Y  673 TYR cc_start: 0.8188 (m-80) cc_final: 0.7702 (m-10)
REVERT: Y  691 PHE cc_start: 0.8755 (m-80) cc_final: 0.8157 (m-80)
REVERT: Y  724 PHE cc_start: 0.7719 (m-10) cc_final: 0.6822 (m-10)
REVERT: Y  745 LEU cc_start: 0.9517 (mt) cc_final: 0.9158 (mm)
REVERT: Y  769 GLN cc_start: 0.7431 (mm110) cc_final: 0.7066 (tp40)
REVERT: Y  773 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8407 (tm-30)
REVERT: Z    1 MET cc_start: 0.8545 (tmm) cc_final: 0.7927 (tmm)
REVERT: Z    5 ILE cc_start: 0.6984 (mm) cc_final: 0.6047 (mm)
REVERT: Z  271 ILE cc_start: 0.9227 (tp) cc_final: 0.8476 (tp)
REVERT: Z  356 TRP cc_start: 0.6986 (t-100) cc_final: 0.6203 (t-100)
REVERT: Z  422 ASN cc_start: 0.8321 (p0) cc_final: 0.8071 (p0)
REVERT: Z  454 ASP cc_start: 0.8967 (t70) cc_final: 0.8693 (t0)
REVERT: Z  505 PHE cc_start: 0.8361 (m-80) cc_final: 0.7550 (m-80)
REVERT: Z  525 LEU cc_start: 0.8531 (pt) cc_final: 0.8302 (pt)
REVERT: Z  611 GLN cc_start: 0.8923 (mp10) cc_final: 0.8304 (mp10)
REVERT: Z  623 GLU cc_start: 0.7821 (tp30) cc_final: 0.6924 (mm-30)
REVERT: Z  632 ASN cc_start: 0.8533 (t0) cc_final: 0.8177 (t0)
REVERT: Z  659 ILE cc_start: 0.9019 (mm) cc_final: 0.8747 (tp)
REVERT: Z  674 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7886 (ttm170)
REVERT: Z  682 PHE cc_start: 0.7068 (p90) cc_final: 0.6826 (p90)
REVERT: Z  689 LYS cc_start: 0.9165 (mmtm) cc_final: 0.8830 (mmmm)
REVERT: Z  714 ASP cc_start: 0.8352 (t0) cc_final: 0.8116 (t0)
REVERT: Z  728 LYS cc_start: 0.6250 (ttpt) cc_final: 0.5976 (tppt)
REVERT: Z  740 GLN cc_start: 0.8980 (mt0) cc_final: 0.8769 (mt0)
REVERT: Z  748 ASP cc_start: 0.8928 (t0) cc_final: 0.8718 (t0)
REVERT: Z  754 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8213 (tm-30)
REVERT: Z  759 ASP cc_start: 0.8573 (p0) cc_final: 0.8133 (p0)
REVERT: Z  764 ARG cc_start: 0.7969 (tpm170) cc_final: 0.6902 (tpm170)
REVERT: Z  767 ILE cc_start: 0.9141 (tt) cc_final: 0.8374 (tt)
  outliers start: 10
  outliers final: 2
  residues processed: 537
  average time/residue: 0.1196
  time to fit residues: 93.6901
Evaluate side-chains
  463 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 460
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 181 optimal weight:    2.9990
   chunk 134 optimal weight:    0.3980
   chunk 37 optimal weight:    6.9990
   chunk 190 optimal weight:    2.9990
   chunk 165 optimal weight:    7.9990
   chunk 97 optimal weight:    0.7980
   chunk 9 optimal weight:   30.0000
   chunk 114 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 145 optimal weight:    5.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
** X 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z 678 ASN
Z 739 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.077660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.065291 restraints weight = 66391.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.067335 restraints weight = 36192.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.068718 restraints weight = 22678.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.069662 restraints weight = 15577.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.070330 restraints weight = 11488.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  16581  Z= 0.176
  Angle     :  0.752  11.777  22523  Z= 0.392
  Chirality :  0.048   0.251   2577
  Planarity :  0.005   0.064   2917
  Dihedral  :  5.834  24.412   2239
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 17.28
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 11.00 %
    Favored  : 88.81 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.74 %
    Favored  : 95.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.54 (0.17), residues: 2055
  helix: -1.01 (0.21), residues: 544
  sheet: -1.78 (0.23), residues: 442
  loop : -3.45 (0.17), residues: 1069

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG Y 274 
 TYR   0.025   0.002   TYR X 219 
 PHE   0.043   0.002   PHE X 505 
 TRP   0.019   0.002   TRP X 356 
 HIS   0.002   0.001   HIS Y 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (16581)
  covalent geometry    : angle       0.75180 (22523)
  hydrogen bonds       : bond        0.04738 (  473)
  hydrogen bonds       : angle       6.33459 ( 1332)

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

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

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  530 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 528
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   20 ASP cc_start: 0.8834 (p0) cc_final: 0.8557 (p0)
REVERT: X   23 GLN cc_start: 0.9022 (mm110) cc_final: 0.8779 (tp-100)
REVERT: X  140 PHE cc_start: 0.7656 (t80) cc_final: 0.7091 (t80)
REVERT: X  141 ILE cc_start: 0.8674 (pt) cc_final: 0.8428 (pt)
REVERT: X  263 LYS cc_start: 0.8348 (tptt) cc_final: 0.8073 (ttmt)
REVERT: X  367 TYR cc_start: 0.8545 (m-80) cc_final: 0.7791 (m-80)
REVERT: X  423 SER cc_start: 0.9144 (t) cc_final: 0.8838 (p)
REVERT: X  425 ARG cc_start: 0.8387 (tpp-160) cc_final: 0.7911 (mmt180)
REVERT: X  522 LEU cc_start: 0.9265 (mm) cc_final: 0.8999 (mm)
REVERT: X  527 MET cc_start: 0.6840 (mtt) cc_final: 0.6098 (mtt)
REVERT: X  531 PHE cc_start: 0.9179 (m-10) cc_final: 0.8795 (m-10)
REVERT: X  551 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8767 (ttpt)
REVERT: X  575 ILE cc_start: 0.9323 (mm) cc_final: 0.8877 (mp)
REVERT: X  615 ILE cc_start: 0.9136 (pt) cc_final: 0.8723 (pt)
REVERT: X  635 ASP cc_start: 0.8898 (m-30) cc_final: 0.8614 (m-30)
REVERT: X  658 ASP cc_start: 0.8271 (p0) cc_final: 0.7699 (p0)
REVERT: X  662 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7258 (pm20)
REVERT: X  665 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8728 (tm-30)
REVERT: X  666 LYS cc_start: 0.9177 (mtmm) cc_final: 0.8682 (mtmm)
REVERT: X  694 LYS cc_start: 0.9016 (tptp) cc_final: 0.8518 (tptt)
REVERT: X  699 GLU cc_start: 0.7958 (mp0) cc_final: 0.7680 (mp0)
REVERT: X  704 ASP cc_start: 0.8416 (t70) cc_final: 0.8211 (t0)
REVERT: X  707 LYS cc_start: 0.8829 (tptp) cc_final: 0.8311 (tptp)
REVERT: X  718 ILE cc_start: 0.8987 (tp) cc_final: 0.8470 (tp)
REVERT: X  729 ASN cc_start: 0.9140 (t0) cc_final: 0.8905 (t0)
REVERT: X  762 ILE cc_start: 0.8526 (pt) cc_final: 0.8157 (pt)
REVERT: X  773 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8135 (tm-30)
REVERT: Y   17 ASP cc_start: 0.8739 (p0) cc_final: 0.8324 (p0)
REVERT: Y  107 LEU cc_start: 0.8702 (tp) cc_final: 0.7827 (tp)
REVERT: Y  220 ILE cc_start: 0.7554 (tp) cc_final: 0.7133 (pt)
REVERT: Y  271 ILE cc_start: 0.8731 (mm) cc_final: 0.8401 (mm)
REVERT: Y  273 ILE cc_start: 0.8642 (tp) cc_final: 0.8074 (tp)
REVERT: Y  328 PHE cc_start: 0.8632 (t80) cc_final: 0.8349 (t80)
REVERT: Y  337 PHE cc_start: 0.7911 (m-80) cc_final: 0.7443 (m-80)
REVERT: Y  415 PHE cc_start: 0.7665 (t80) cc_final: 0.7061 (t80)
REVERT: Y  522 LEU cc_start: 0.9181 (tp) cc_final: 0.8967 (tp)
REVERT: Y  527 MET cc_start: 0.8440 (ppp) cc_final: 0.7659 (tmm)
REVERT: Y  539 ASP cc_start: 0.7776 (t70) cc_final: 0.7429 (t70)
REVERT: Y  549 MET cc_start: 0.7870 (mtm) cc_final: 0.7523 (mmm)
REVERT: Y  566 ASP cc_start: 0.8269 (p0) cc_final: 0.8048 (p0)
REVERT: Y  619 LEU cc_start: 0.8748 (mm) cc_final: 0.8024 (tp)
REVERT: Y  634 ASP cc_start: 0.8231 (p0) cc_final: 0.7495 (p0)
REVERT: Y  643 THR cc_start: 0.9330 (m) cc_final: 0.9097 (t)
REVERT: Y  645 ILE cc_start: 0.8940 (pt) cc_final: 0.8719 (pt)
REVERT: Y  662 GLU cc_start: 0.9028 (pt0) cc_final: 0.8389 (pt0)
REVERT: Y  673 TYR cc_start: 0.8164 (m-80) cc_final: 0.7542 (m-10)
REVERT: Y  691 PHE cc_start: 0.8672 (m-80) cc_final: 0.8468 (m-80)
REVERT: Y  753 ARG cc_start: 0.8118 (ttt90) cc_final: 0.7851 (ttt90)
REVERT: Y  769 GLN cc_start: 0.7272 (mm110) cc_final: 0.6839 (tp40)
REVERT: Y  773 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8399 (tm-30)
REVERT: Z    1 MET cc_start: 0.8758 (tmm) cc_final: 0.8022 (tmm)
REVERT: Z    5 ILE cc_start: 0.6738 (mm) cc_final: 0.5754 (mm)
REVERT: Z  263 LYS cc_start: 0.9186 (mppt) cc_final: 0.8959 (mmtm)
REVERT: Z  356 TRP cc_start: 0.7304 (t-100) cc_final: 0.6361 (t-100)
REVERT: Z  422 ASN cc_start: 0.8595 (p0) cc_final: 0.8322 (p0)
REVERT: Z  494 LEU cc_start: 0.8538 (mp) cc_final: 0.8246 (tt)
REVERT: Z  505 PHE cc_start: 0.8468 (m-80) cc_final: 0.7590 (m-80)
REVERT: Z  581 ILE cc_start: 0.9182 (pt) cc_final: 0.8434 (pt)
REVERT: Z  611 GLN cc_start: 0.8947 (mp10) cc_final: 0.8334 (mp10)
REVERT: Z  623 GLU cc_start: 0.7695 (tp30) cc_final: 0.6962 (tp30)
REVERT: Z  631 MET cc_start: 0.8189 (tmm) cc_final: 0.7917 (tmm)
REVERT: Z  632 ASN cc_start: 0.8629 (t0) cc_final: 0.8183 (t0)
REVERT: Z  659 ILE cc_start: 0.9048 (mm) cc_final: 0.8728 (tp)
REVERT: Z  666 LYS cc_start: 0.8933 (mmmm) cc_final: 0.8705 (mppt)
REVERT: Z  674 ARG cc_start: 0.8232 (mtm-85) cc_final: 0.7547 (mtt90)
REVERT: Z  689 LYS cc_start: 0.9186 (mmtm) cc_final: 0.8891 (mmmm)
REVERT: Z  714 ASP cc_start: 0.8527 (t0) cc_final: 0.8283 (t0)
REVERT: Z  721 ILE cc_start: 0.9394 (mt) cc_final: 0.8773 (mt)
REVERT: Z  728 LYS cc_start: 0.6278 (ttpt) cc_final: 0.5779 (tppt)
REVERT: Z  729 ASN cc_start: 0.8919 (t0) cc_final: 0.8363 (t0)
REVERT: Z  733 ASN cc_start: 0.9089 (m-40) cc_final: 0.8669 (m-40)
REVERT: Z  748 ASP cc_start: 0.8947 (t0) cc_final: 0.8740 (t0)
REVERT: Z  754 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8221 (tm-30)
REVERT: Z  759 ASP cc_start: 0.8573 (p0) cc_final: 0.8257 (p0)
REVERT: Z  764 ARG cc_start: 0.8072 (tpm170) cc_final: 0.6887 (tpm170)
REVERT: Z  767 ILE cc_start: 0.9155 (tt) cc_final: 0.8474 (tt)
  outliers start: 2
  outliers final: 0
  residues processed: 529
  average time/residue: 0.1192
  time to fit residues: 92.1747
Evaluate side-chains
  453 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 452
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 16 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 176 optimal weight:    0.7980
   chunk 196 optimal weight:    0.1980
   chunk 113 optimal weight:    7.9990
   chunk 193 optimal weight:    0.9980
   chunk 157 optimal weight:    0.0470
   chunk 139 optimal weight:    0.9990
   chunk 162 optimal weight:   10.0000
   overall best weight:    0.6080

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

Flipped N/Q/H residues before XYZ refinement:
X 757 ASN
Y 324 ASN
** Y 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z 760 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.080493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.068217 restraints weight = 64931.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.070291 restraints weight = 35478.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.071698 restraints weight = 22227.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.072629 restraints weight = 15220.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.073319 restraints weight = 11240.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  16581  Z= 0.137
  Angle     :  0.735  11.843  22523  Z= 0.378
  Chirality :  0.048   0.196   2577
  Planarity :  0.005   0.067   2917
  Dihedral  :  5.691  24.297   2239
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 11.09 %
    Favored  : 88.71 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.52 %
    Favored  : 95.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.42 (0.17), residues: 2055
  helix: -1.02 (0.21), residues: 545
  sheet: -1.56 (0.24), residues: 446
  loop : -3.40 (0.17), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG Z 502 
 TYR   0.022   0.001   TYR Z 461 
 PHE   0.057   0.002   PHE X 505 
 TRP   0.022   0.001   TRP X 356 
 HIS   0.002   0.001   HIS X 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (16581)
  covalent geometry    : angle       0.73534 (22523)
  hydrogen bonds       : bond        0.04204 (  473)
  hydrogen bonds       : angle       6.09946 ( 1332)

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

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

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  533 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 531
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   14 TYR cc_start: 0.7405 (p90) cc_final: 0.7192 (p90)
REVERT: X   20 ASP cc_start: 0.8717 (p0) cc_final: 0.8474 (p0)
REVERT: X   22 ILE cc_start: 0.9013 (mm) cc_final: 0.8767 (mm)
REVERT: X   23 GLN cc_start: 0.8875 (mm110) cc_final: 0.8649 (tp-100)
REVERT: X   25 ILE cc_start: 0.8670 (tp) cc_final: 0.8431 (tp)
REVERT: X  140 PHE cc_start: 0.7204 (t80) cc_final: 0.6870 (t80)
REVERT: X  141 ILE cc_start: 0.8526 (pt) cc_final: 0.8314 (pt)
REVERT: X  142 ASP cc_start: 0.6132 (m-30) cc_final: 0.5374 (m-30)
REVERT: X  263 LYS cc_start: 0.8235 (tptt) cc_final: 0.7963 (ttmt)
REVERT: X  367 TYR cc_start: 0.8487 (m-80) cc_final: 0.7778 (m-80)
REVERT: X  371 LEU cc_start: 0.7566 (pt) cc_final: 0.6958 (pt)
REVERT: X  423 SER cc_start: 0.9182 (t) cc_final: 0.8840 (p)
REVERT: X  425 ARG cc_start: 0.8260 (tpp-160) cc_final: 0.7810 (mmt180)
REVERT: X  512 ILE cc_start: 0.9178 (mm) cc_final: 0.8967 (mm)
REVERT: X  530 MET cc_start: 0.8819 (tpt) cc_final: 0.8616 (tpp)
REVERT: X  551 LYS cc_start: 0.9074 (ttmt) cc_final: 0.8679 (ttpt)
REVERT: X  624 MET cc_start: 0.7423 (mtp) cc_final: 0.6414 (mtt)
REVERT: X  644 LYS cc_start: 0.8379 (tttp) cc_final: 0.8159 (tttm)
REVERT: X  665 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8510 (tm-30)
REVERT: X  666 LYS cc_start: 0.9145 (mtmm) cc_final: 0.8607 (mtmm)
REVERT: X  694 LYS cc_start: 0.8620 (tptp) cc_final: 0.8253 (tptt)
REVERT: X  696 ASP cc_start: 0.8841 (t0) cc_final: 0.8616 (t0)
REVERT: X  699 GLU cc_start: 0.7806 (mp0) cc_final: 0.7571 (mp0)
REVERT: X  703 PHE cc_start: 0.7296 (p90) cc_final: 0.6031 (p90)
REVERT: X  707 LYS cc_start: 0.8822 (tptp) cc_final: 0.8520 (tptp)
REVERT: X  718 ILE cc_start: 0.8930 (tp) cc_final: 0.8353 (tp)
REVERT: X  729 ASN cc_start: 0.9083 (t0) cc_final: 0.8878 (t0)
REVERT: X  773 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8124 (tm-30)
REVERT: Y   17 ASP cc_start: 0.8774 (p0) cc_final: 0.8380 (p0)
REVERT: Y   42 GLN cc_start: 0.9009 (mp10) cc_final: 0.8631 (mp10)
REVERT: Y   69 TYR cc_start: 0.6534 (m-80) cc_final: 0.5710 (m-80)
REVERT: Y  106 ILE cc_start: 0.8709 (tp) cc_final: 0.8451 (tp)
REVERT: Y  107 LEU cc_start: 0.8649 (tp) cc_final: 0.7988 (tp)
REVERT: Y  207 ILE cc_start: 0.7798 (pt) cc_final: 0.7425 (pt)
REVERT: Y  220 ILE cc_start: 0.7467 (tp) cc_final: 0.7145 (pt)
REVERT: Y  271 ILE cc_start: 0.8779 (mm) cc_final: 0.8528 (mm)
REVERT: Y  273 ILE cc_start: 0.8659 (tp) cc_final: 0.8035 (tp)
REVERT: Y  328 PHE cc_start: 0.8594 (t80) cc_final: 0.8336 (t80)
REVERT: Y  380 CYS cc_start: 0.8651 (m) cc_final: 0.8092 (t)
REVERT: Y  415 PHE cc_start: 0.7589 (t80) cc_final: 0.6981 (t80)
REVERT: Y  463 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7493 (mm-30)
REVERT: Y  522 LEU cc_start: 0.9162 (tp) cc_final: 0.8931 (tp)
REVERT: Y  527 MET cc_start: 0.8425 (ppp) cc_final: 0.8185 (ppp)
REVERT: Y  539 ASP cc_start: 0.7751 (t70) cc_final: 0.7390 (t70)
REVERT: Y  549 MET cc_start: 0.7705 (mtm) cc_final: 0.7293 (mmm)
REVERT: Y  619 LEU cc_start: 0.8768 (mm) cc_final: 0.8295 (tp)
REVERT: Y  634 ASP cc_start: 0.7772 (p0) cc_final: 0.7105 (p0)
REVERT: Y  662 GLU cc_start: 0.8879 (pt0) cc_final: 0.8276 (pt0)
REVERT: Y  673 TYR cc_start: 0.8125 (m-80) cc_final: 0.7614 (m-80)
REVERT: Y  691 PHE cc_start: 0.8803 (m-80) cc_final: 0.8094 (m-80)
REVERT: Y  724 PHE cc_start: 0.6888 (m-10) cc_final: 0.6576 (m-10)
REVERT: Y  743 ASN cc_start: 0.8832 (m-40) cc_final: 0.8565 (m-40)
REVERT: Y  753 ARG cc_start: 0.7812 (ttt90) cc_final: 0.7409 (ttt90)
REVERT: Y  769 GLN cc_start: 0.7528 (mm110) cc_final: 0.6980 (tp40)
REVERT: Y  773 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8264 (tm-30)
REVERT: Z    1 MET cc_start: 0.8720 (tmm) cc_final: 0.8023 (tmm)
REVERT: Z    5 ILE cc_start: 0.6882 (mm) cc_final: 0.6131 (mt)
REVERT: Z  271 ILE cc_start: 0.9365 (tp) cc_final: 0.8786 (tp)
REVERT: Z  356 TRP cc_start: 0.7152 (t-100) cc_final: 0.6437 (t-100)
REVERT: Z  497 GLN cc_start: 0.7511 (mp10) cc_final: 0.7086 (mp10)
REVERT: Z  611 GLN cc_start: 0.8909 (mp10) cc_final: 0.8366 (mp10)
REVERT: Z  617 ARG cc_start: 0.8662 (ttm110) cc_final: 0.8436 (ttm110)
REVERT: Z  623 GLU cc_start: 0.7548 (tp30) cc_final: 0.6939 (tp30)
REVERT: Z  626 THR cc_start: 0.8637 (p) cc_final: 0.8387 (p)
REVERT: Z  632 ASN cc_start: 0.8552 (t0) cc_final: 0.7599 (p0)
REVERT: Z  659 ILE cc_start: 0.9022 (mm) cc_final: 0.8694 (tp)
REVERT: Z  683 GLU cc_start: 0.7419 (pp20) cc_final: 0.6794 (pp20)
REVERT: Z  689 LYS cc_start: 0.9086 (mmtm) cc_final: 0.8796 (mmmm)
REVERT: Z  727 LEU cc_start: 0.9224 (mm) cc_final: 0.9023 (mp)
REVERT: Z  728 LYS cc_start: 0.5964 (ttpt) cc_final: 0.5646 (tppt)
REVERT: Z  748 ASP cc_start: 0.8942 (t0) cc_final: 0.8633 (t70)
REVERT: Z  754 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8168 (tm-30)
REVERT: Z  759 ASP cc_start: 0.8452 (p0) cc_final: 0.7881 (p0)
REVERT: Z  767 ILE cc_start: 0.9089 (tt) cc_final: 0.8707 (tt)
  outliers start: 2
  outliers final: 0
  residues processed: 533
  average time/residue: 0.1175
  time to fit residues: 92.0432
Evaluate side-chains
  456 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 456
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 154 optimal weight:    7.9990
   chunk 3 optimal weight:    6.9990
   chunk 180 optimal weight:    9.9990
   chunk 40 optimal weight:    6.9990
   chunk 134 optimal weight:    8.9990
   chunk 107 optimal weight:    5.9990
   chunk 112 optimal weight:    1.9990
   chunk 110 optimal weight:    2.9990
   chunk 127 optimal weight:    0.0570
   chunk 77 optimal weight:    4.9990
   chunk 124 optimal weight:    2.9990
   overall best weight:    2.6106

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

Flipped N/Q/H residues before XYZ refinement:
** X 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 611 GLN
X 757 ASN
Y 266 GLN
Y 457 ASN
Z 760 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.076843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.064598 restraints weight = 65696.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.066599 restraints weight = 36097.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.067925 restraints weight = 22756.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.068873 restraints weight = 15740.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.069532 restraints weight = 11657.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3160
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3160
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.3232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  16581  Z= 0.206
  Angle     :  0.771  13.181  22523  Z= 0.400
  Chirality :  0.048   0.235   2577
  Planarity :  0.006   0.085   2917
  Dihedral  :  5.840  26.552   2239
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 18.34
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 12.02 %
    Favored  : 87.83 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  3.49 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.45 (0.17), residues: 2055
  helix: -1.02 (0.21), residues: 550
  sheet: -1.61 (0.23), residues: 477
  loop : -3.46 (0.17), residues: 1028

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG Y 274 
 TYR   0.028   0.002   TYR X 673 
 PHE   0.043   0.002   PHE X 755 
 TRP   0.021   0.002   TRP X 356 
 HIS   0.003   0.001   HIS X 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (16581)
  covalent geometry    : angle       0.77069 (22523)
  hydrogen bonds       : bond        0.04597 (  473)
  hydrogen bonds       : angle       6.07032 ( 1332)

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

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

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  502 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 501
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   20 ASP cc_start: 0.8764 (p0) cc_final: 0.8539 (p0)
REVERT: X   23 GLN cc_start: 0.8913 (mm110) cc_final: 0.8669 (tp-100)
REVERT: X   25 ILE cc_start: 0.8795 (tp) cc_final: 0.8481 (tp)
REVERT: X   81 TRP cc_start: 0.7329 (m100) cc_final: 0.5684 (m100)
REVERT: X  140 PHE cc_start: 0.7347 (t80) cc_final: 0.7023 (t80)
REVERT: X  168 MET cc_start: 0.7903 (pmm) cc_final: 0.7614 (pmm)
REVERT: X  423 SER cc_start: 0.9232 (t) cc_final: 0.8908 (p)
REVERT: X  425 ARG cc_start: 0.8384 (tpp-160) cc_final: 0.8118 (tpp-160)
REVERT: X  530 MET cc_start: 0.8859 (tpt) cc_final: 0.8616 (tpp)
REVERT: X  544 MET cc_start: 0.8999 (ppp) cc_final: 0.8260 (ppp)
REVERT: X  551 LYS cc_start: 0.9080 (ttmt) cc_final: 0.8718 (ttpt)
REVERT: X  631 MET cc_start: 0.8776 (tpp) cc_final: 0.8363 (tpp)
REVERT: X  662 GLU cc_start: 0.8286 (pm20) cc_final: 0.7789 (pm20)
REVERT: X  665 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8480 (tm-30)
REVERT: X  666 LYS cc_start: 0.9142 (mtmm) cc_final: 0.8571 (mtmm)
REVERT: X  673 TYR cc_start: 0.7828 (m-80) cc_final: 0.7413 (m-80)
REVERT: X  694 LYS cc_start: 0.8575 (tptp) cc_final: 0.8202 (tptt)
REVERT: X  699 GLU cc_start: 0.7885 (mp0) cc_final: 0.7625 (mp0)
REVERT: X  704 ASP cc_start: 0.8399 (t0) cc_final: 0.8094 (t0)
REVERT: X  707 LYS cc_start: 0.8870 (tptp) cc_final: 0.8373 (tptp)
REVERT: X  718 ILE cc_start: 0.8979 (tp) cc_final: 0.8296 (tp)
REVERT: X  729 ASN cc_start: 0.9116 (t0) cc_final: 0.8883 (t0)
REVERT: X  762 ILE cc_start: 0.8656 (pt) cc_final: 0.8227 (pt)
REVERT: X  768 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8320 (tm-30)
REVERT: X  769 GLN cc_start: 0.8563 (pp30) cc_final: 0.8332 (pp30)
REVERT: X  773 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8285 (tm-30)
REVERT: Y    4 LEU cc_start: 0.7897 (pt) cc_final: 0.6071 (pt)
REVERT: Y   12 ASN cc_start: 0.7920 (m-40) cc_final: 0.7694 (m-40)
REVERT: Y   17 ASP cc_start: 0.8813 (p0) cc_final: 0.8335 (p0)
REVERT: Y   42 GLN cc_start: 0.9081 (mp10) cc_final: 0.8647 (mp10)
REVERT: Y  107 LEU cc_start: 0.8663 (tp) cc_final: 0.8017 (tp)
REVERT: Y  220 ILE cc_start: 0.7590 (tp) cc_final: 0.7258 (pt)
REVERT: Y  273 ILE cc_start: 0.8696 (tp) cc_final: 0.8014 (tp)
REVERT: Y  328 PHE cc_start: 0.8528 (t80) cc_final: 0.8257 (t80)
REVERT: Y  337 PHE cc_start: 0.7899 (m-80) cc_final: 0.7632 (m-80)
REVERT: Y  380 CYS cc_start: 0.8512 (m) cc_final: 0.8229 (m)
REVERT: Y  415 PHE cc_start: 0.7657 (t80) cc_final: 0.7161 (t80)
REVERT: Y  519 ASP cc_start: 0.7780 (m-30) cc_final: 0.7156 (m-30)
REVERT: Y  527 MET cc_start: 0.8463 (ppp) cc_final: 0.7697 (tmm)
REVERT: Y  539 ASP cc_start: 0.7828 (t70) cc_final: 0.7587 (t70)
REVERT: Y  549 MET cc_start: 0.7852 (mtm) cc_final: 0.7488 (mmm)
REVERT: Y  619 LEU cc_start: 0.8853 (mm) cc_final: 0.8148 (tp)
REVERT: Y  634 ASP cc_start: 0.8031 (p0) cc_final: 0.7212 (p0)
REVERT: Y  662 GLU cc_start: 0.8901 (pt0) cc_final: 0.8309 (pt0)
REVERT: Y  673 TYR cc_start: 0.8214 (m-80) cc_final: 0.7716 (m-10)
REVERT: Y  743 ASN cc_start: 0.8912 (m-40) cc_final: 0.8597 (m-40)
REVERT: Y  753 ARG cc_start: 0.7902 (ttt90) cc_final: 0.7575 (ttt90)
REVERT: Y  769 GLN cc_start: 0.7288 (mm110) cc_final: 0.6757 (tp40)
REVERT: Y  773 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8323 (tm-30)
REVERT: Z    1 MET cc_start: 0.8818 (tmm) cc_final: 0.8579 (tmm)
REVERT: Z    5 ILE cc_start: 0.6814 (mm) cc_final: 0.6154 (mt)
REVERT: Z  271 ILE cc_start: 0.9500 (tp) cc_final: 0.8885 (tp)
REVERT: Z  273 ILE cc_start: 0.9085 (tp) cc_final: 0.8866 (tp)
REVERT: Z  276 LYS cc_start: 0.8977 (tptm) cc_final: 0.8480 (ttmm)
REVERT: Z  371 LEU cc_start: 0.9212 (tp) cc_final: 0.8896 (tp)
REVERT: Z  505 PHE cc_start: 0.8626 (m-80) cc_final: 0.7860 (m-80)
REVERT: Z  611 GLN cc_start: 0.9032 (mp10) cc_final: 0.8437 (mp10)
REVERT: Z  623 GLU cc_start: 0.7457 (tp30) cc_final: 0.6929 (mm-30)
REVERT: Z  632 ASN cc_start: 0.8630 (t0) cc_final: 0.7962 (t0)
REVERT: Z  689 LYS cc_start: 0.9200 (mmtm) cc_final: 0.8979 (mmmm)
REVERT: Z  724 PHE cc_start: 0.8381 (t80) cc_final: 0.8174 (t80)
REVERT: Z  748 ASP cc_start: 0.8939 (t0) cc_final: 0.8716 (t0)
REVERT: Z  759 ASP cc_start: 0.8349 (p0) cc_final: 0.7960 (p0)
REVERT: Z  764 ARG cc_start: 0.7854 (tpm170) cc_final: 0.7606 (tpm170)
REVERT: Z  767 ILE cc_start: 0.9105 (tt) cc_final: 0.8642 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 502
  average time/residue: 0.1144
  time to fit residues: 84.8343
Evaluate side-chains
  435 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 435
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 172 optimal weight:    3.9990
   chunk 189 optimal weight:    9.9990
   chunk 92 optimal weight:    5.9990
   chunk 96 optimal weight:   10.0000
   chunk 193 optimal weight:    1.9990
   chunk 125 optimal weight:    0.0870
   chunk 157 optimal weight:    0.8980
   chunk 149 optimal weight:    7.9990
   chunk 25 optimal weight:    9.9990
   overall best weight:    1.7964

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

Flipped N/Q/H residues before XYZ refinement:
X   8 GLN
X 611 GLN
X 757 ASN
Y 324 ASN
** Y 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.078004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.065803 restraints weight = 65633.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.067826 restraints weight = 35879.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.069187 restraints weight = 22538.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.070129 restraints weight = 15486.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.070749 restraints weight = 11391.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3176
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3176
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  16581  Z= 0.169
  Angle     :  0.760  10.040  22523  Z= 0.392
  Chirality :  0.048   0.241   2577
  Planarity :  0.006   0.133   2917
  Dihedral  :  5.867  26.685   2239
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 17.59
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 11.92 %
    Favored  : 87.93 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  2.34 %
    Favored  : 97.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.46 (0.17), residues: 2055
  helix: -1.09 (0.21), residues: 558
  sheet: -1.74 (0.22), residues: 513
  loop : -3.39 (0.18), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG Z 618 
 TYR   0.038   0.002   TYR X 461 
 PHE   0.032   0.002   PHE Y 505 
 TRP   0.020   0.002   TRP X 356 
 HIS   0.002   0.001   HIS X 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (16581)
  covalent geometry    : angle       0.76010 (22523)
  hydrogen bonds       : bond        0.04343 (  473)
  hydrogen bonds       : angle       6.01699 ( 1332)

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

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

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  505 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 504
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   20 ASP cc_start: 0.8818 (p0) cc_final: 0.8579 (p0)
REVERT: X   23 GLN cc_start: 0.8869 (mm110) cc_final: 0.8597 (tp-100)
REVERT: X  140 PHE cc_start: 0.7293 (t80) cc_final: 0.6853 (t80)
REVERT: X  141 ILE cc_start: 0.8538 (pt) cc_final: 0.8317 (pt)
REVERT: X  142 ASP cc_start: 0.5965 (m-30) cc_final: 0.5118 (m-30)
REVERT: X  371 LEU cc_start: 0.7656 (pt) cc_final: 0.7228 (pt)
REVERT: X  423 SER cc_start: 0.9238 (t) cc_final: 0.8923 (p)
REVERT: X  512 ILE cc_start: 0.9218 (mm) cc_final: 0.9007 (mm)
REVERT: X  530 MET cc_start: 0.8844 (tpt) cc_final: 0.8608 (tpp)
REVERT: X  544 MET cc_start: 0.8972 (ppp) cc_final: 0.8264 (ppp)
REVERT: X  551 LYS cc_start: 0.9059 (ttmt) cc_final: 0.8716 (ttpt)
REVERT: X  624 MET cc_start: 0.7669 (mtp) cc_final: 0.7052 (mtt)
REVERT: X  631 MET cc_start: 0.8795 (tpp) cc_final: 0.8581 (mmm)
REVERT: X  635 ASP cc_start: 0.8982 (m-30) cc_final: 0.8693 (m-30)
REVERT: X  658 ASP cc_start: 0.8277 (p0) cc_final: 0.8073 (p0)
REVERT: X  665 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8481 (tm-30)
REVERT: X  666 LYS cc_start: 0.9082 (mtmm) cc_final: 0.8554 (mtmm)
REVERT: X  694 LYS cc_start: 0.8531 (tptp) cc_final: 0.8155 (tptt)
REVERT: X  699 GLU cc_start: 0.7874 (mp0) cc_final: 0.7629 (mp0)
REVERT: X  704 ASP cc_start: 0.8433 (t0) cc_final: 0.8060 (t0)
REVERT: X  707 LYS cc_start: 0.8979 (tptp) cc_final: 0.8608 (tptp)
REVERT: X  718 ILE cc_start: 0.8981 (tp) cc_final: 0.8373 (tp)
REVERT: X  729 ASN cc_start: 0.9128 (t0) cc_final: 0.8902 (t0)
REVERT: X  762 ILE cc_start: 0.8587 (pt) cc_final: 0.8175 (pt)
REVERT: X  768 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8299 (tm-30)
REVERT: X  769 GLN cc_start: 0.8570 (pp30) cc_final: 0.8301 (pp30)
REVERT: X  773 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8285 (tm-30)
REVERT: Y    4 LEU cc_start: 0.7230 (pt) cc_final: 0.6267 (pt)
REVERT: Y    8 GLN cc_start: 0.8319 (mp10) cc_final: 0.7716 (mp10)
REVERT: Y    9 LEU cc_start: 0.8813 (mt) cc_final: 0.8609 (mt)
REVERT: Y   17 ASP cc_start: 0.8674 (p0) cc_final: 0.8145 (p0)
REVERT: Y   21 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8712 (tm-30)
REVERT: Y   42 GLN cc_start: 0.9024 (mp10) cc_final: 0.8585 (mp10)
REVERT: Y  106 ILE cc_start: 0.8699 (tp) cc_final: 0.8226 (tp)
REVERT: Y  107 LEU cc_start: 0.8727 (tp) cc_final: 0.8344 (tp)
REVERT: Y  220 ILE cc_start: 0.7622 (tp) cc_final: 0.7094 (pt)
REVERT: Y  273 ILE cc_start: 0.8717 (tp) cc_final: 0.8013 (tp)
REVERT: Y  328 PHE cc_start: 0.8506 (t80) cc_final: 0.8232 (t80)
REVERT: Y  337 PHE cc_start: 0.7922 (m-80) cc_final: 0.7544 (m-80)
REVERT: Y  342 PHE cc_start: 0.7314 (t80) cc_final: 0.7056 (t80)
REVERT: Y  380 CYS cc_start: 0.8339 (m) cc_final: 0.8124 (m)
REVERT: Y  415 PHE cc_start: 0.7568 (t80) cc_final: 0.7112 (t80)
REVERT: Y  471 ILE cc_start: 0.9549 (tp) cc_final: 0.9307 (tp)
REVERT: Y  527 MET cc_start: 0.8402 (ppp) cc_final: 0.7865 (tmm)
REVERT: Y  539 ASP cc_start: 0.7860 (t70) cc_final: 0.7613 (t70)
REVERT: Y  549 MET cc_start: 0.7778 (mtm) cc_final: 0.7411 (tmm)
REVERT: Y  619 LEU cc_start: 0.8776 (mm) cc_final: 0.7982 (tp)
REVERT: Y  634 ASP cc_start: 0.7700 (p0) cc_final: 0.7117 (p0)
REVERT: Y  645 ILE cc_start: 0.9005 (pt) cc_final: 0.8777 (pt)
REVERT: Y  662 GLU cc_start: 0.8910 (pt0) cc_final: 0.8312 (pt0)
REVERT: Y  673 TYR cc_start: 0.8129 (m-80) cc_final: 0.7590 (m-10)
REVERT: Y  769 GLN cc_start: 0.7279 (mm110) cc_final: 0.6787 (tp40)
REVERT: Y  773 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8207 (tm-30)
REVERT: Z    1 MET cc_start: 0.8749 (tmm) cc_final: 0.8549 (tmm)
REVERT: Z    5 ILE cc_start: 0.6254 (mm) cc_final: 0.5631 (mt)
REVERT: Z    8 GLN cc_start: 0.7840 (pm20) cc_final: 0.7357 (pm20)
REVERT: Z  271 ILE cc_start: 0.9144 (tp) cc_final: 0.8884 (tp)
REVERT: Z  276 LYS cc_start: 0.8973 (tptm) cc_final: 0.8417 (ttmm)
REVERT: Z  425 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7881 (mtp85)
REVERT: Z  497 GLN cc_start: 0.7844 (mp10) cc_final: 0.7442 (mp10)
REVERT: Z  611 GLN cc_start: 0.9020 (mp10) cc_final: 0.8563 (mp10)
REVERT: Z  623 GLU cc_start: 0.7429 (tp30) cc_final: 0.6890 (mm-30)
REVERT: Z  631 MET cc_start: 0.8094 (tmm) cc_final: 0.7880 (tmm)
REVERT: Z  632 ASN cc_start: 0.8568 (t0) cc_final: 0.7928 (t0)
REVERT: Z  659 ILE cc_start: 0.8973 (tp) cc_final: 0.8754 (tp)
REVERT: Z  689 LYS cc_start: 0.9157 (mmtm) cc_final: 0.8908 (mmmm)
REVERT: Z  723 ASP cc_start: 0.7537 (p0) cc_final: 0.7332 (p0)
REVERT: Z  724 PHE cc_start: 0.8323 (t80) cc_final: 0.8083 (t80)
REVERT: Z  748 ASP cc_start: 0.8955 (t0) cc_final: 0.8711 (t0)
REVERT: Z  759 ASP cc_start: 0.8275 (p0) cc_final: 0.7939 (p0)
REVERT: Z  764 ARG cc_start: 0.7754 (tpm170) cc_final: 0.7377 (tpm170)
REVERT: Z  767 ILE cc_start: 0.9119 (tt) cc_final: 0.8682 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 504
  average time/residue: 0.1165
  time to fit residues: 86.8041
Evaluate side-chains
  439 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 438
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 171 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   chunk 103 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 176 optimal weight:    7.9990
   chunk 74 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 108 optimal weight:    7.9990
   chunk 164 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
X   8 GLN
** X 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 611 GLN
X 757 ASN
Y  31 GLN
Y 251 ASN
Y 324 ASN
Y 477 ASN
** Y 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z 739 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.074971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.062796 restraints weight = 66001.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.064753 restraints weight = 36029.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.066072 restraints weight = 22586.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.066982 restraints weight = 15553.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.067590 restraints weight = 11468.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3110
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3110
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.3766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078  16581  Z= 0.240
  Angle     :  0.814   9.974  22523  Z= 0.424
  Chirality :  0.049   0.233   2577
  Planarity :  0.006   0.109   2917
  Dihedral  :  6.106  27.004   2239
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 20.57
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 13.48 %
    Favored  : 86.37 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  2.89 %
    Favored  : 97.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.60 (0.17), residues: 2055
  helix: -1.10 (0.20), residues: 563
  sheet: -1.96 (0.21), residues: 533
  loop : -3.50 (0.18), residues: 959

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG Y 753 
 TYR   0.027   0.002   TYR Z 461 
 PHE   0.032   0.002   PHE X 505 
 TRP   0.026   0.002   TRP X 356 
 HIS   0.004   0.001   HIS Z 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00543 (16581)
  covalent geometry    : angle       0.81399 (22523)
  hydrogen bonds       : bond        0.04873 (  473)
  hydrogen bonds       : angle       6.13716 ( 1332)

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

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

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  493 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 492
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   20 ASP cc_start: 0.8763 (p0) cc_final: 0.8493 (p0)
REVERT: X   23 GLN cc_start: 0.8883 (mm110) cc_final: 0.8631 (tp-100)
REVERT: X   24 GLU cc_start: 0.8613 (pp20) cc_final: 0.8339 (tm-30)
REVERT: X   81 TRP cc_start: 0.7529 (m100) cc_final: 0.5873 (m100)
REVERT: X  140 PHE cc_start: 0.7385 (t80) cc_final: 0.7112 (t80)
REVERT: X  168 MET cc_start: 0.7973 (pmm) cc_final: 0.7744 (pmm)
REVERT: X  265 MET cc_start: 0.8556 (mmm) cc_final: 0.8350 (mmm)
REVERT: X  530 MET cc_start: 0.8866 (tpt) cc_final: 0.8641 (tpp)
REVERT: X  544 MET cc_start: 0.8720 (ppp) cc_final: 0.8479 (ppp)
REVERT: X  551 LYS cc_start: 0.9063 (ttmt) cc_final: 0.8725 (ttpt)
REVERT: X  635 ASP cc_start: 0.8837 (m-30) cc_final: 0.8547 (m-30)
REVERT: X  665 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8686 (tm-30)
REVERT: X  694 LYS cc_start: 0.8592 (tptp) cc_final: 0.8149 (tptp)
REVERT: X  699 GLU cc_start: 0.8001 (mp0) cc_final: 0.7779 (mp0)
REVERT: X  704 ASP cc_start: 0.8594 (t0) cc_final: 0.8362 (t0)
REVERT: X  707 LYS cc_start: 0.9066 (tptp) cc_final: 0.8713 (tptp)
REVERT: X  729 ASN cc_start: 0.9201 (t0) cc_final: 0.8956 (t0)
REVERT: X  754 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8527 (tm-30)
REVERT: X  762 ILE cc_start: 0.8597 (pt) cc_final: 0.8114 (pt)
REVERT: X  768 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8354 (tm-30)
REVERT: Y    4 LEU cc_start: 0.7335 (pt) cc_final: 0.6244 (pt)
REVERT: Y    8 GLN cc_start: 0.8278 (mp10) cc_final: 0.7461 (mp10)
REVERT: Y    9 LEU cc_start: 0.8873 (mt) cc_final: 0.8548 (mt)
REVERT: Y   17 ASP cc_start: 0.8801 (p0) cc_final: 0.8285 (p0)
REVERT: Y   21 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8849 (tm-30)
REVERT: Y  220 ILE cc_start: 0.7683 (tp) cc_final: 0.7446 (pt)
REVERT: Y  273 ILE cc_start: 0.8832 (tp) cc_final: 0.8008 (tp)
REVERT: Y  328 PHE cc_start: 0.8599 (t80) cc_final: 0.8288 (t80)
REVERT: Y  337 PHE cc_start: 0.8008 (m-80) cc_final: 0.7742 (m-80)
REVERT: Y  344 VAL cc_start: 0.8999 (t) cc_final: 0.8704 (t)
REVERT: Y  415 PHE cc_start: 0.7501 (t80) cc_final: 0.7213 (t80)
REVERT: Y  471 ILE cc_start: 0.9448 (tp) cc_final: 0.9142 (tp)
REVERT: Y  519 ASP cc_start: 0.7600 (m-30) cc_final: 0.6971 (m-30)
REVERT: Y  527 MET cc_start: 0.8457 (ppp) cc_final: 0.7810 (tmm)
REVERT: Y  549 MET cc_start: 0.7952 (mtm) cc_final: 0.7581 (tmm)
REVERT: Y  624 MET cc_start: 0.7729 (tmm) cc_final: 0.7360 (tmm)
REVERT: Y  662 GLU cc_start: 0.8912 (pt0) cc_final: 0.8308 (pt0)
REVERT: Y  673 TYR cc_start: 0.8188 (m-80) cc_final: 0.7705 (m-10)
REVERT: Y  754 GLU cc_start: 0.8647 (pp20) cc_final: 0.8442 (pp20)
REVERT: Y  773 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8317 (tm-30)
REVERT: Z    5 ILE cc_start: 0.6526 (mm) cc_final: 0.5975 (mt)
REVERT: Z    8 GLN cc_start: 0.8043 (pm20) cc_final: 0.7556 (pm20)
REVERT: Z  271 ILE cc_start: 0.9340 (tp) cc_final: 0.9109 (tp)
REVERT: Z  276 LYS cc_start: 0.9029 (tptm) cc_final: 0.8464 (ttmm)
REVERT: Z  357 ASP cc_start: 0.8362 (m-30) cc_final: 0.7527 (m-30)
REVERT: Z  371 LEU cc_start: 0.9194 (tp) cc_final: 0.8894 (tp)
REVERT: Z  425 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7780 (mtp85)
REVERT: Z  497 GLN cc_start: 0.7728 (mp10) cc_final: 0.7305 (mp10)
REVERT: Z  611 GLN cc_start: 0.9089 (mp10) cc_final: 0.8554 (mp10)
REVERT: Z  623 GLU cc_start: 0.7307 (tp30) cc_final: 0.7039 (mm-30)
REVERT: Z  631 MET cc_start: 0.8160 (tmm) cc_final: 0.7918 (tmm)
REVERT: Z  659 ILE cc_start: 0.9030 (tp) cc_final: 0.8799 (tp)
REVERT: Z  674 ARG cc_start: 0.9032 (ptp-110) cc_final: 0.8500 (ptp90)
REVERT: Z  689 LYS cc_start: 0.9227 (mmtm) cc_final: 0.8983 (mmmm)
REVERT: Z  748 ASP cc_start: 0.8978 (t0) cc_final: 0.8721 (t0)
REVERT: Z  754 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8248 (tm-30)
REVERT: Z  759 ASP cc_start: 0.8407 (p0) cc_final: 0.8034 (p0)
  outliers start: 1
  outliers final: 1
  residues processed: 493
  average time/residue: 0.1154
  time to fit residues: 84.4566
Evaluate side-chains
  426 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 425
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 72 optimal weight:    0.0970
   chunk 123 optimal weight:    7.9990
   chunk 78 optimal weight:    0.4980
   chunk 120 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 116 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 11 optimal weight:   20.0000
   chunk 175 optimal weight:    5.9990
   chunk 74 optimal weight:    0.3980
   chunk 150 optimal weight:    3.9990
   overall best weight:    1.3982

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

Flipped N/Q/H residues before XYZ refinement:
X   8 GLN
X 611 GLN
X 757 ASN
** Y 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 324 ASN
Y 477 ASN
Y 597 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.077635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.065503 restraints weight = 65576.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.067493 restraints weight = 35936.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.068853 restraints weight = 22547.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.069773 restraints weight = 15468.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.070422 restraints weight = 11397.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.3905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  16581  Z= 0.156
  Angle     :  0.794  11.439  22523  Z= 0.405
  Chirality :  0.048   0.223   2577
  Planarity :  0.006   0.081   2917
  Dihedral  :  5.953  26.199   2239
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 17.90
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 11.78 %
    Favored  : 88.08 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.69 %
    Favored  : 98.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.47 (0.17), residues: 2055
  helix: -0.97 (0.21), residues: 555
  sheet: -1.82 (0.22), residues: 508
  loop : -3.43 (0.18), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG X 443 
 TYR   0.037   0.002   TYR X 461 
 PHE   0.038   0.002   PHE X 755 
 TRP   0.036   0.002   TRP X 356 
 HIS   0.002   0.001   HIS X 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (16581)
  covalent geometry    : angle       0.79409 (22523)
  hydrogen bonds       : bond        0.04340 (  473)
  hydrogen bonds       : angle       5.91383 ( 1332)

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

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

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  500 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 497
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X    8 GLN cc_start: 0.8638 (pt0) cc_final: 0.7668 (pp30)
REVERT: X   20 ASP cc_start: 0.8705 (p0) cc_final: 0.8431 (p0)
REVERT: X   23 GLN cc_start: 0.8775 (mm110) cc_final: 0.8538 (tp-100)
REVERT: X  140 PHE cc_start: 0.7163 (t80) cc_final: 0.6824 (t80)
REVERT: X  141 ILE cc_start: 0.8495 (pt) cc_final: 0.8254 (pt)
REVERT: X  142 ASP cc_start: 0.5862 (m-30) cc_final: 0.5033 (m-30)
REVERT: X  371 LEU cc_start: 0.7589 (pt) cc_final: 0.7249 (pt)
REVERT: X  375 LEU cc_start: 0.8826 (mm) cc_final: 0.8549 (mt)
REVERT: X  423 SER cc_start: 0.9092 (t) cc_final: 0.8800 (p)
REVERT: X  512 ILE cc_start: 0.9221 (mm) cc_final: 0.8984 (mm)
REVERT: X  635 ASP cc_start: 0.8763 (m-30) cc_final: 0.8213 (m-30)
REVERT: X  644 LYS cc_start: 0.8617 (tttp) cc_final: 0.8347 (tttm)
REVERT: X  658 ASP cc_start: 0.8504 (p0) cc_final: 0.7973 (p0)
REVERT: X  662 GLU cc_start: 0.8261 (pm20) cc_final: 0.7802 (pm20)
REVERT: X  665 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8431 (tm-30)
REVERT: X  694 LYS cc_start: 0.8621 (tptp) cc_final: 0.8162 (tptt)
REVERT: X  718 ILE cc_start: 0.9070 (tp) cc_final: 0.8551 (tp)
REVERT: X  729 ASN cc_start: 0.9191 (t0) cc_final: 0.8969 (t0)
REVERT: X  754 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8452 (tm-30)
REVERT: X  762 ILE cc_start: 0.8347 (pt) cc_final: 0.7909 (pt)
REVERT: X  768 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8173 (tm-30)
REVERT: Y    9 LEU cc_start: 0.8859 (mt) cc_final: 0.8636 (mt)
REVERT: Y   12 ASN cc_start: 0.7993 (m-40) cc_final: 0.7786 (m-40)
REVERT: Y   17 ASP cc_start: 0.8746 (p0) cc_final: 0.8286 (p0)
REVERT: Y   21 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8690 (tm-30)
REVERT: Y  107 LEU cc_start: 0.8765 (tp) cc_final: 0.8449 (tp)
REVERT: Y  220 ILE cc_start: 0.7573 (tp) cc_final: 0.7060 (pt)
REVERT: Y  263 LYS cc_start: 0.8420 (ttpp) cc_final: 0.7635 (ttpp)
REVERT: Y  265 MET cc_start: 0.8853 (mmm) cc_final: 0.8560 (mmm)
REVERT: Y  273 ILE cc_start: 0.8710 (tp) cc_final: 0.7921 (tp)
REVERT: Y  328 PHE cc_start: 0.8632 (t80) cc_final: 0.8340 (t80)
REVERT: Y  337 PHE cc_start: 0.7887 (m-80) cc_final: 0.7656 (m-80)
REVERT: Y  342 PHE cc_start: 0.7386 (t80) cc_final: 0.7151 (t80)
REVERT: Y  412 SER cc_start: 0.8810 (m) cc_final: 0.8477 (p)
REVERT: Y  415 PHE cc_start: 0.7645 (t80) cc_final: 0.7217 (t80)
REVERT: Y  514 MET cc_start: 0.7135 (ptt) cc_final: 0.6859 (ptp)
REVERT: Y  519 ASP cc_start: 0.7435 (m-30) cc_final: 0.6936 (m-30)
REVERT: Y  527 MET cc_start: 0.8387 (ppp) cc_final: 0.7846 (ppp)
REVERT: Y  549 MET cc_start: 0.7803 (mtm) cc_final: 0.7296 (tmm)
REVERT: Y  634 ASP cc_start: 0.7988 (p0) cc_final: 0.7002 (p0)
REVERT: Y  662 GLU cc_start: 0.8900 (pt0) cc_final: 0.8291 (pt0)
REVERT: Y  673 TYR cc_start: 0.8135 (m-80) cc_final: 0.7634 (m-10)
REVERT: Y  690 PHE cc_start: 0.8494 (m-80) cc_final: 0.8292 (m-80)
REVERT: Y  732 ASP cc_start: 0.6943 (t0) cc_final: 0.6651 (t70)
REVERT: Y  753 ARG cc_start: 0.7859 (ttt90) cc_final: 0.7629 (ttt90)
REVERT: Y  773 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8183 (tm-30)
REVERT: Z    5 ILE cc_start: 0.6329 (mm) cc_final: 0.5783 (mt)
REVERT: Z    8 GLN cc_start: 0.7815 (pm20) cc_final: 0.7534 (pm20)
REVERT: Z  271 ILE cc_start: 0.9330 (tp) cc_final: 0.8545 (tp)
REVERT: Z  357 ASP cc_start: 0.8268 (m-30) cc_final: 0.7462 (m-30)
REVERT: Z  371 LEU cc_start: 0.9232 (tp) cc_final: 0.8874 (tp)
REVERT: Z  425 ARG cc_start: 0.8267 (mtp85) cc_final: 0.7868 (mtp85)
REVERT: Z  497 GLN cc_start: 0.7921 (mp10) cc_final: 0.7537 (mp10)
REVERT: Z  528 PHE cc_start: 0.8593 (t80) cc_final: 0.8386 (t80)
REVERT: Z  544 MET cc_start: 0.8339 (mmm) cc_final: 0.8066 (mpp)
REVERT: Z  611 GLN cc_start: 0.9022 (mp10) cc_final: 0.8560 (mp10)
REVERT: Z  631 MET cc_start: 0.8132 (tmm) cc_final: 0.7835 (tmm)
REVERT: Z  674 ARG cc_start: 0.8950 (ptp-110) cc_final: 0.8682 (ptp90)
REVERT: Z  689 LYS cc_start: 0.9218 (mmtm) cc_final: 0.9014 (mmmm)
REVERT: Z  739 GLN cc_start: 0.8254 (tp40) cc_final: 0.7995 (tp40)
REVERT: Z  748 ASP cc_start: 0.8942 (t0) cc_final: 0.8718 (t0)
REVERT: Z  754 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8089 (pp20)
REVERT: Z  755 PHE cc_start: 0.9042 (t80) cc_final: 0.8767 (t80)
REVERT: Z  759 ASP cc_start: 0.8289 (p0) cc_final: 0.7984 (p0)
  outliers start: 3
  outliers final: 1
  residues processed: 500
  average time/residue: 0.1133
  time to fit residues: 84.2926
Evaluate side-chains
  435 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 434
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 131 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 162 optimal weight:    6.9990
   chunk 171 optimal weight:    8.9990
   chunk 202 optimal weight:    3.9990
   chunk 204 optimal weight:    2.9990
   chunk 93 optimal weight:   10.0000
   chunk 175 optimal weight:    5.9990
   chunk 143 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
X 221 ASN
X 757 ASN
** Y 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 324 ASN
** Y 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.078595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.066283 restraints weight = 65569.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.068308 restraints weight = 35934.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.069663 restraints weight = 22607.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.070611 restraints weight = 15576.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.071268 restraints weight = 11500.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.4038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  16581  Z= 0.156
  Angle     :  0.804  10.933  22523  Z= 0.411
  Chirality :  0.049   0.229   2577
  Planarity :  0.006   0.068   2917
  Dihedral  :  5.859  25.908   2239
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 17.03
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 12.60 %
    Favored  : 87.25 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.54 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.40 (0.17), residues: 2055
  helix: -0.98 (0.21), residues: 557
  sheet: -1.77 (0.22), residues: 519
  loop : -3.37 (0.18), residues: 979

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG X 443 
 TYR   0.027   0.002   TYR Z 461 
 PHE   0.041   0.002   PHE X 505 
 TRP   0.032   0.002   TRP X 356 
 HIS   0.002   0.001   HIS Z 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (16581)
  covalent geometry    : angle       0.80381 (22523)
  hydrogen bonds       : bond        0.04193 (  473)
  hydrogen bonds       : angle       5.89172 ( 1332)

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

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

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  495 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 494
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   20 ASP cc_start: 0.8662 (p0) cc_final: 0.8413 (p0)
REVERT: X   23 GLN cc_start: 0.8825 (mm110) cc_final: 0.8569 (tp-100)
REVERT: X   25 ILE cc_start: 0.8586 (tp) cc_final: 0.8375 (tp)
REVERT: X   81 TRP cc_start: 0.7338 (m100) cc_final: 0.5637 (m100)
REVERT: X  140 PHE cc_start: 0.7064 (t80) cc_final: 0.6726 (t80)
REVERT: X  141 ILE cc_start: 0.8489 (pt) cc_final: 0.8249 (pt)
REVERT: X  142 ASP cc_start: 0.6120 (m-30) cc_final: 0.5385 (m-30)
REVERT: X  168 MET cc_start: 0.7947 (pmm) cc_final: 0.7430 (pmm)
REVERT: X  276 LYS cc_start: 0.6260 (mttt) cc_final: 0.6035 (mmtp)
REVERT: X  290 LYS cc_start: 0.8063 (mptt) cc_final: 0.7812 (mmtm)
REVERT: X  371 LEU cc_start: 0.7554 (pt) cc_final: 0.7171 (pt)
REVERT: X  375 LEU cc_start: 0.8847 (mm) cc_final: 0.8575 (mt)
REVERT: X  423 SER cc_start: 0.9096 (t) cc_final: 0.8848 (p)
REVERT: X  425 ARG cc_start: 0.8670 (tpp-160) cc_final: 0.8416 (tpp-160)
REVERT: X  512 ILE cc_start: 0.9169 (mm) cc_final: 0.8930 (mm)
REVERT: X  527 MET cc_start: 0.7574 (mtt) cc_final: 0.7357 (mtt)
REVERT: X  551 LYS cc_start: 0.9214 (ttmt) cc_final: 0.8938 (ttpt)
REVERT: X  631 MET cc_start: 0.8709 (tpp) cc_final: 0.8171 (tpp)
REVERT: X  635 ASP cc_start: 0.8760 (m-30) cc_final: 0.8206 (m-30)
REVERT: X  644 LYS cc_start: 0.8505 (tttp) cc_final: 0.8230 (tttm)
REVERT: X  665 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8470 (tm-30)
REVERT: X  694 LYS cc_start: 0.8465 (tptp) cc_final: 0.8260 (tptt)
REVERT: X  707 LYS cc_start: 0.9057 (tptp) cc_final: 0.8738 (tptp)
REVERT: X  754 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8413 (tm-30)
REVERT: Y    4 LEU cc_start: 0.7322 (pt) cc_final: 0.6283 (pt)
REVERT: Y    8 GLN cc_start: 0.8335 (mp10) cc_final: 0.7867 (mp10)
REVERT: Y   17 ASP cc_start: 0.8791 (p0) cc_final: 0.8283 (p0)
REVERT: Y   21 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8691 (tm-30)
REVERT: Y  107 LEU cc_start: 0.8792 (tp) cc_final: 0.8434 (tp)
REVERT: Y  220 ILE cc_start: 0.7459 (tp) cc_final: 0.7227 (pt)
REVERT: Y  263 LYS cc_start: 0.8414 (ttpp) cc_final: 0.7931 (ttpp)
REVERT: Y  328 PHE cc_start: 0.8690 (t80) cc_final: 0.8350 (t80)
REVERT: Y  342 PHE cc_start: 0.7427 (t80) cc_final: 0.7188 (t80)
REVERT: Y  380 CYS cc_start: 0.8372 (m) cc_final: 0.7870 (t)
REVERT: Y  412 SER cc_start: 0.8903 (m) cc_final: 0.8700 (p)
REVERT: Y  415 PHE cc_start: 0.7658 (t80) cc_final: 0.7206 (t80)
REVERT: Y  519 ASP cc_start: 0.7495 (m-30) cc_final: 0.6933 (m-30)
REVERT: Y  527 MET cc_start: 0.8365 (ppp) cc_final: 0.7596 (ppp)
REVERT: Y  634 ASP cc_start: 0.7964 (p0) cc_final: 0.7152 (p0)
REVERT: Y  645 ILE cc_start: 0.9075 (pt) cc_final: 0.8872 (pt)
REVERT: Y  662 GLU cc_start: 0.8926 (pt0) cc_final: 0.8345 (pt0)
REVERT: Y  673 TYR cc_start: 0.8130 (m-80) cc_final: 0.7565 (m-10)
REVERT: Y  732 ASP cc_start: 0.6883 (t0) cc_final: 0.6545 (t70)
REVERT: Y  773 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8198 (tm-30)
REVERT: Z    5 ILE cc_start: 0.6064 (mm) cc_final: 0.5601 (mm)
REVERT: Z  271 ILE cc_start: 0.9446 (tp) cc_final: 0.8810 (tp)
REVERT: Z  357 ASP cc_start: 0.8254 (m-30) cc_final: 0.7338 (m-30)
REVERT: Z  371 LEU cc_start: 0.9246 (tp) cc_final: 0.8886 (tp)
REVERT: Z  425 ARG cc_start: 0.8278 (mtp85) cc_final: 0.7861 (mtp85)
REVERT: Z  497 GLN cc_start: 0.7967 (mp10) cc_final: 0.7594 (mp10)
REVERT: Z  514 MET cc_start: 0.7716 (mtp) cc_final: 0.7208 (mtp)
REVERT: Z  544 MET cc_start: 0.8382 (mmm) cc_final: 0.8129 (mmm)
REVERT: Z  611 GLN cc_start: 0.9006 (mp10) cc_final: 0.8554 (mp10)
REVERT: Z  631 MET cc_start: 0.8102 (tmm) cc_final: 0.7844 (tmm)
REVERT: Z  662 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7356 (mp0)
REVERT: Z  674 ARG cc_start: 0.8907 (ptp-110) cc_final: 0.8566 (ptp90)
REVERT: Z  689 LYS cc_start: 0.9218 (mmtm) cc_final: 0.9012 (mmmm)
REVERT: Z  739 GLN cc_start: 0.8168 (tp40) cc_final: 0.7876 (tp40)
REVERT: Z  748 ASP cc_start: 0.8937 (t0) cc_final: 0.8729 (t0)
REVERT: Z  754 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8050 (pp20)
REVERT: Z  755 PHE cc_start: 0.8988 (t80) cc_final: 0.8312 (t80)
REVERT: Z  759 ASP cc_start: 0.8336 (p0) cc_final: 0.8115 (p0)
REVERT: Z  760 ASN cc_start: 0.7482 (m-40) cc_final: 0.7018 (m-40)
REVERT: Z  763 ILE cc_start: 0.9361 (pt) cc_final: 0.8936 (pt)
REVERT: Z  764 ARG cc_start: 0.7697 (tpm170) cc_final: 0.5755 (tpm170)
  outliers start: 1
  outliers final: 0
  residues processed: 494
  average time/residue: 0.1145
  time to fit residues: 84.4031
Evaluate side-chains
  423 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 423
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 116 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 167 optimal weight:    3.9990
   chunk 178 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 112 optimal weight:    2.9990
   chunk 191 optimal weight:    0.0470
   chunk 86 optimal weight:    6.9990
   chunk 44 optimal weight:    0.3980
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.8080

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

Flipped N/Q/H residues before XYZ refinement:
X   8 GLN
X 221 ASN
X 757 ASN
** Y  12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 324 ASN
** Y 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.079893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.067491 restraints weight = 64741.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.069537 restraints weight = 35707.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.070917 restraints weight = 22520.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.071867 restraints weight = 15521.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.072538 restraints weight = 11475.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3217
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3217 r_free = 0.3217    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3216
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.4191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.101  16581  Z= 0.146
  Angle     :  0.796  10.823  22523  Z= 0.404
  Chirality :  0.048   0.222   2577
  Planarity :  0.005   0.068   2917
  Dihedral  :  5.740  26.131   2239
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 16.69
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.85 %
    Favored  : 89.00 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.38 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.37 (0.17), residues: 2055
  helix: -1.01 (0.21), residues: 555
  sheet: -1.54 (0.23), residues: 494
  loop : -3.41 (0.18), residues: 1006

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG X   7 
 TYR   0.033   0.002   TYR Z 461 
 PHE   0.043   0.002   PHE X 505 
 TRP   0.029   0.002   TRP X 356 
 HIS   0.002   0.000   HIS Z 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (16581)
  covalent geometry    : angle       0.79552 (22523)
  hydrogen bonds       : bond        0.04132 (  473)
  hydrogen bonds       : angle       5.82815 ( 1332)

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

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

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4110 Ramachandran restraints generated.
    2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  488 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 487
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   25 ILE cc_start: 0.8419 (tp) cc_final: 0.8158 (tp)
REVERT: X  116 ASN cc_start: 0.8328 (t0) cc_final: 0.8105 (m-40)
REVERT: X  140 PHE cc_start: 0.6936 (t80) cc_final: 0.6710 (t80)
REVERT: X  141 ILE cc_start: 0.8448 (pt) cc_final: 0.8209 (pt)
REVERT: X  142 ASP cc_start: 0.5982 (m-30) cc_final: 0.5187 (m-30)
REVERT: X  290 LYS cc_start: 0.8090 (mptt) cc_final: 0.7882 (mmtm)
REVERT: X  371 LEU cc_start: 0.7538 (pt) cc_final: 0.7175 (pt)
REVERT: X  423 SER cc_start: 0.9105 (t) cc_final: 0.8832 (p)
REVERT: X  425 ARG cc_start: 0.8620 (tpp-160) cc_final: 0.8357 (tpp-160)
REVERT: X  512 ILE cc_start: 0.9189 (mm) cc_final: 0.8919 (mm)
REVERT: X  530 MET cc_start: 0.8834 (tpt) cc_final: 0.8607 (tpp)
REVERT: X  551 LYS cc_start: 0.9187 (ttmt) cc_final: 0.8905 (ttpt)
REVERT: X  631 MET cc_start: 0.8692 (tpp) cc_final: 0.8222 (tpp)
REVERT: X  635 ASP cc_start: 0.8803 (m-30) cc_final: 0.8546 (m-30)
REVERT: X  644 LYS cc_start: 0.8437 (tttp) cc_final: 0.8079 (tttm)
REVERT: X  665 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8507 (tm-30)
REVERT: X  694 LYS cc_start: 0.8612 (tptp) cc_final: 0.8381 (tptt)
REVERT: X  696 ASP cc_start: 0.8854 (t0) cc_final: 0.8635 (t0)
REVERT: X  707 LYS cc_start: 0.9040 (tptp) cc_final: 0.8736 (tptp)
REVERT: X  728 LYS cc_start: 0.8684 (mptt) cc_final: 0.8470 (mmtm)
REVERT: X  754 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8344 (tm-30)
REVERT: Y    4 LEU cc_start: 0.7246 (pt) cc_final: 0.6297 (pt)
REVERT: Y    8 GLN cc_start: 0.8410 (mp10) cc_final: 0.7954 (mp10)
REVERT: Y   17 ASP cc_start: 0.8820 (p0) cc_final: 0.8308 (p0)
REVERT: Y  175 TYR cc_start: 0.6843 (m-80) cc_final: 0.6401 (m-80)
REVERT: Y  220 ILE cc_start: 0.7704 (tp) cc_final: 0.7209 (pt)
REVERT: Y  263 LYS cc_start: 0.8294 (ttpp) cc_final: 0.7832 (ttpp)
REVERT: Y  273 ILE cc_start: 0.8781 (tp) cc_final: 0.8027 (tp)
REVERT: Y  328 PHE cc_start: 0.8658 (t80) cc_final: 0.8341 (t80)
REVERT: Y  337 PHE cc_start: 0.7960 (m-80) cc_final: 0.7541 (m-80)
REVERT: Y  342 PHE cc_start: 0.7366 (t80) cc_final: 0.7139 (t80)
REVERT: Y  380 CYS cc_start: 0.8478 (m) cc_final: 0.7932 (t)
REVERT: Y  415 PHE cc_start: 0.7663 (t80) cc_final: 0.7176 (t80)
REVERT: Y  500 GLU cc_start: 0.7500 (pt0) cc_final: 0.6718 (pp20)
REVERT: Y  527 MET cc_start: 0.8360 (ppp) cc_final: 0.7538 (ppp)
REVERT: Y  634 ASP cc_start: 0.7879 (p0) cc_final: 0.7090 (p0)
REVERT: Y  662 GLU cc_start: 0.8934 (pt0) cc_final: 0.8395 (pt0)
REVERT: Y  673 TYR cc_start: 0.8044 (m-80) cc_final: 0.7506 (m-80)
REVERT: Y  729 ASN cc_start: 0.6546 (m-40) cc_final: 0.6320 (t0)
REVERT: Y  753 ARG cc_start: 0.7765 (ttt90) cc_final: 0.7521 (ttt90)
REVERT: Y  773 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8165 (tm-30)
REVERT: Z    5 ILE cc_start: 0.6009 (mm) cc_final: 0.5661 (mt)
REVERT: Z  271 ILE cc_start: 0.9511 (tp) cc_final: 0.8858 (tp)
REVERT: Z  357 ASP cc_start: 0.8161 (m-30) cc_final: 0.7159 (m-30)
REVERT: Z  371 LEU cc_start: 0.9238 (tp) cc_final: 0.8883 (tp)
REVERT: Z  425 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7884 (mtp85)
REVERT: Z  497 GLN cc_start: 0.7927 (mp10) cc_final: 0.7559 (mp10)
REVERT: Z  514 MET cc_start: 0.7690 (mtp) cc_final: 0.7303 (mtp)
REVERT: Z  527 MET cc_start: 0.8116 (mmm) cc_final: 0.7492 (mmt)
REVERT: Z  544 MET cc_start: 0.8357 (mmm) cc_final: 0.8108 (mmm)
REVERT: Z  611 GLN cc_start: 0.8977 (mp10) cc_final: 0.8539 (mp10)
REVERT: Z  631 MET cc_start: 0.8046 (tmm) cc_final: 0.7830 (tmm)
REVERT: Z  662 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7296 (mp0)
REVERT: Z  674 ARG cc_start: 0.8844 (ptp-110) cc_final: 0.8548 (ptp90)
REVERT: Z  739 GLN cc_start: 0.8231 (tp40) cc_final: 0.7933 (tp40)
REVERT: Z  755 PHE cc_start: 0.8916 (t80) cc_final: 0.8174 (t80)
REVERT: Z  759 ASP cc_start: 0.8317 (p0) cc_final: 0.8040 (p0)
REVERT: Z  763 ILE cc_start: 0.9395 (pt) cc_final: 0.9018 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 487
  average time/residue: 0.1131
  time to fit residues: 81.2333
Evaluate side-chains
  425 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 425
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 85 optimal weight:   20.0000
   chunk 73 optimal weight:    1.9990
   chunk 98 optimal weight:    9.9990
   chunk 194 optimal weight:    2.9990
   chunk 14 optimal weight:    0.4980
   chunk 122 optimal weight:    0.0870
   chunk 107 optimal weight:    6.9990
   chunk 168 optimal weight:    0.7980
   chunk 130 optimal weight:    0.9980
   chunk 143 optimal weight:    4.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
X   8 GLN
X 221 ASN
X 757 ASN
** X 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 251 ASN
** Y 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 324 ASN
** Y 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.080970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.068417 restraints weight = 64667.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.070487 restraints weight = 35872.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.071883 restraints weight = 22706.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.072817 restraints weight = 15661.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.073526 restraints weight = 11657.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3237
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3237
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.4307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  16581  Z= 0.142
  Angle     :  0.794  10.818  22523  Z= 0.401
  Chirality :  0.048   0.233   2577
  Planarity :  0.005   0.067   2917
  Dihedral  :  5.606  25.281   2239
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 11.44 %
    Favored  : 88.42 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.38 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.26 (0.18), residues: 2055
  helix: -0.93 (0.21), residues: 552
  sheet: -1.45 (0.23), residues: 492
  loop : -3.35 (0.18), residues: 1011

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG Y 766 
 TYR   0.027   0.002   TYR Z 461 
 PHE   0.042   0.002   PHE X 505 
 TRP   0.034   0.002   TRP X 356 
 HIS   0.002   0.001   HIS Z 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (16581)
  covalent geometry    : angle       0.79352 (22523)
  hydrogen bonds       : bond        0.03971 (  473)
  hydrogen bonds       : angle       5.78465 ( 1332)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2841.78 seconds
wall clock time: 49 minutes 57.49 seconds (2997.49 seconds total)