Starting phenix.real_space_refine
on Sun Aug 24 03:37:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wkx_37610/08_2025/8wkx_37610.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wkx_37610/08_2025/8wkx_37610.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wkx_37610/08_2025/8wkx_37610.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wkx_37610/08_2025/8wkx_37610.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wkx_37610/08_2025/8wkx_37610.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wkx_37610/08_2025/8wkx_37610.cif"
  }
  resolution = 4.15
  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=  -0.001 sd=   0.033
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      64      5.16       5
     C   10708      2.51       5
     N    2676      2.21       5
     O    3107      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  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: 16555
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1002, 8347
          Classifications: {'peptide': 1002}
          Link IDs: {'PTRANS': 19, 'TRANS': 982}
    Chain: "E"
      Number of atoms: 8208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 986, 8208
          Classifications: {'peptide': 986}
          Link IDs: {'PTRANS': 19, 'TRANS': 966}
          Chain breaks: 2
  Time building chain proxies: 4.22, per 1000 atoms: 0.25
  Number of scatterers: 16555
  At special positions: 0
  Unit cell: (101.65, 129.47, 156.22, 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      64     16.00
     O    3107      8.00
     N    2676      7.00
     C   10708      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: 1.59
  Conformation dependent library (CDL) restraints added in 791.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3784

  Finding SS restraints...
    Secondary structure from input PDB file:
      110 helices and 4 sheets defined
      61.9% alpha, 2.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 22
    Processing helix  chain 'A' and resid 23 through 39
    Processing helix  chain 'A' and resid 48 through 54
      removed outlier: 3.643A  pdb=" N   THR A  52 " --> pdb=" O   ALA A  48 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU A  53 " --> pdb=" O   GLY A  49 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   SER A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 48 through 54'
    Processing helix  chain 'A' and resid 58 through 72
    Processing helix  chain 'A' and resid 80 through 95
      removed outlier: 3.977A  pdb=" N   LEU A  85 " --> pdb=" O   SER A  81 " (cutoff:3.500A)
      Proline residue:  A  88  - end of helix
    Processing helix  chain 'A' and resid 96 through 109
      removed outlier: 4.005A  pdb=" N   PHE A 100 " --> pdb=" O   GLY A  96 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN A 109 " --> pdb=" O   LYS A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 123
      removed outlier: 4.219A  pdb=" N   ASP A 119 " --> pdb=" O   ASN A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 146
    Processing helix  chain 'A' and resid 154 through 160
    Processing helix  chain 'A' and resid 186 through 192
    Processing helix  chain 'A' and resid 192 through 197
    Processing helix  chain 'A' and resid 197 through 211
      removed outlier: 3.780A  pdb=" N   ALA A 209 " --> pdb=" O   LYS A 205 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   THR A 210 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   HIS A 211 " --> pdb=" O   ILE A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 234
      removed outlier: 3.658A  pdb=" N   LYS A 234 " --> pdb=" O   ASN A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 265
    Processing helix  chain 'A' and resid 281 through 296
    Processing helix  chain 'A' and resid 306 through 317
      removed outlier: 3.987A  pdb=" N   ASP A 310 " --> pdb=" O   ASP A 306 " (cutoff:3.500A)
      removed outlier: 5.212A  pdb=" N   ILE A 312 " --> pdb=" O   VAL A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 322
    Processing helix  chain 'A' and resid 329 through 334
      removed outlier: 3.513A  pdb=" N   VAL A 333 " --> pdb=" O   ASP A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 366
    Processing helix  chain 'A' and resid 374 through 392
    Processing helix  chain 'A' and resid 411 through 416
      removed outlier: 4.013A  pdb=" N   HIS A 415 " --> pdb=" O   SER A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 427
      removed outlier: 4.133A  pdb=" N   GLU A 427 " --> pdb=" O   LYS A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 443
      removed outlier: 3.585A  pdb=" N   ASP A 435 " --> pdb=" O   SER A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 461
      removed outlier: 3.684A  pdb=" N   ASN A 461 " --> pdb=" O   ASN A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 496
    Processing helix  chain 'A' and resid 508 through 520
      removed outlier: 3.758A  pdb=" N   LEU A 512 " --> pdb=" O   THR A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 529
    Processing helix  chain 'A' and resid 532 through 538
      removed outlier: 3.640A  pdb=" N   LYS A 538 " --> pdb=" O   GLU A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 547
      removed outlier: 4.396A  pdb=" N   PHE A 544 " --> pdb=" O   ILE A 541 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   SER A 546 " --> pdb=" O   GLU A 543 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASP A 547 " --> pdb=" O   PHE A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 570
      removed outlier: 3.872A  pdb=" N   VAL A 556 " --> pdb=" O   TYR A 552 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   LYS A 557 " --> pdb=" O   ASP A 553 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   LEU A 558 " --> pdb=" O   ASP A 554 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ASN A 563 " --> pdb=" O   PHE A 559 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   GLU A 568 " --> pdb=" O   LYS A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 594
    Processing helix  chain 'A' and resid 610 through 622
      removed outlier: 3.644A  pdb=" N   SER A 617 " --> pdb=" O   ARG A 613 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   LEU A 618 " --> pdb=" O   ASN A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 626
    Processing helix  chain 'A' and resid 648 through 659
    Processing helix  chain 'A' and resid 660 through 669
    Processing helix  chain 'A' and resid 682 through 701
      removed outlier: 4.076A  pdb=" N   ALA A 701 " --> pdb=" O   LYS A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 723
      removed outlier: 3.726A  pdb=" N   LYS A 717 " --> pdb=" O   ILE A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 729 through 742
      removed outlier: 3.635A  pdb=" N   GLY A 734 " --> pdb=" O   GLU A 730 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   LYS A 735 " --> pdb=" O   GLU A 731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 765
    Processing helix  chain 'A' and resid 769 through 786
      removed outlier: 4.302A  pdb=" N   SER A 773 " --> pdb=" O   LYS A 769 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   ILE A 774 " --> pdb=" O   SER A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 812
      removed outlier: 6.721A  pdb=" N   ILE A 808 " --> pdb=" O   TYR A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 826
    Processing helix  chain 'A' and resid 831 through 841
    Processing helix  chain 'A' and resid 842 through 845
    Processing helix  chain 'A' and resid 846 through 855
      removed outlier: 3.630A  pdb=" N   SER A 855 " --> pdb=" O   SER A 851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 872
    Processing helix  chain 'A' and resid 878 through 903
      removed outlier: 3.509A  pdb=" N   ILE A 897 " --> pdb=" O   LYS A 893 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 922
      removed outlier: 4.045A  pdb=" N   THR A 915 " --> pdb=" O   ASP A 911 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   TRP A 919 " --> pdb=" O   THR A 915 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   TYR A 920 " --> pdb=" O   PHE A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 928 through 934
    Processing helix  chain 'A' and resid 937 through 945
    Processing helix  chain 'A' and resid 950 through 954
      removed outlier: 4.313A  pdb=" N   LYS A 953 " --> pdb=" O   ASP A 950 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 955 through 962
      removed outlier: 3.828A  pdb=" N   TRP A 958 " --> pdb=" O   ILE A 955 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   TYR A 962 " --> pdb=" O   LEU A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 972
      removed outlier: 3.831A  pdb=" N   GLY A 972 " --> pdb=" O   GLY A 968 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 976 through 990
      removed outlier: 3.810A  pdb=" N   VAL A 983 " --> pdb=" O   HIS A 979 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LEU A 984 " --> pdb=" O   VAL A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1003
    Processing helix  chain 'E' and resid 16 through 20
    Processing helix  chain 'E' and resid 26 through 39
    Processing helix  chain 'E' and resid 48 through 54
    Processing helix  chain 'E' and resid 58 through 71
      removed outlier: 3.651A  pdb=" N   LEU E  62 " --> pdb=" O   GLN E  58 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 82 through 93
      removed outlier: 3.693A  pdb=" N   ILE E  87 " --> pdb=" O   GLU E  83 " (cutoff:3.500A)
      Proline residue:  E  88  - end of helix
      removed outlier: 3.623A  pdb=" N   PHE E  91 " --> pdb=" O   ILE E  87 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 96 through 109
      removed outlier: 4.023A  pdb=" N   PHE E 100 " --> pdb=" O   GLY E  96 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 115 through 124
      removed outlier: 3.841A  pdb=" N   ASP E 119 " --> pdb=" O   ASN E 115 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 136 through 146
      removed outlier: 3.662A  pdb=" N   CYS E 142 " --> pdb=" O   ILE E 138 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   TRP E 143 " --> pdb=" O   ASP E 139 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   LYS E 144 " --> pdb=" O   THR E 140 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ARG E 145 " --> pdb=" O   ALA E 141 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 179 through 183
      removed outlier: 3.695A  pdb=" N   ASN E 182 " --> pdb=" O   LYS E 179 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   VAL E 183 " --> pdb=" O   GLY E 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 179 through 183'
    Processing helix  chain 'E' and resid 186 through 192
      removed outlier: 3.501A  pdb=" N   ASN E 192 " --> pdb=" O   ASP E 188 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 192 through 197
    Processing helix  chain 'E' and resid 197 through 211
      removed outlier: 3.861A  pdb=" N   SER E 201 " --> pdb=" O   TYR E 197 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ASN E 202 " --> pdb=" O   PRO E 198 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   LEU E 203 " --> pdb=" O   LEU E 199 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 222 through 236
      removed outlier: 4.115A  pdb=" N   LYS E 234 " --> pdb=" O   ASN E 230 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 254 through 265
      removed outlier: 3.730A  pdb=" N   LEU E 258 " --> pdb=" O   GLU E 254 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 281 through 295
      removed outlier: 3.772A  pdb=" N   LEU E 293 " --> pdb=" O   VAL E 289 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLU E 295 " --> pdb=" O   ASP E 291 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 312 through 317
    Processing helix  chain 'E' and resid 326 through 334
      removed outlier: 3.731A  pdb=" N   LEU E 330 " --> pdb=" O   ARG E 326 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LYS E 331 " --> pdb=" O   LYS E 327 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   HIS E 332 " --> pdb=" O   ILE E 328 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 355 through 366
      removed outlier: 4.240A  pdb=" N   GLU E 365 " --> pdb=" O   PHE E 361 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   SER E 366 " --> pdb=" O   GLU E 362 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 366 through 372
      removed outlier: 4.182A  pdb=" N   LYS E 372 " --> pdb=" O   ASP E 368 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 374 through 392
    Processing helix  chain 'E' and resid 396 through 400
      removed outlier: 4.071A  pdb=" N   ALA E 400 " --> pdb=" O   ALA E 397 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 411 through 416
      removed outlier: 3.885A  pdb=" N   HIS E 415 " --> pdb=" O   SER E 411 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 418 through 427
    Processing helix  chain 'E' and resid 431 through 446
    Processing helix  chain 'E' and resid 452 through 465
      removed outlier: 3.854A  pdb=" N   SER E 456 " --> pdb=" O   TYR E 452 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 470 through 492
    Processing helix  chain 'E' and resid 493 through 500
      removed outlier: 3.751A  pdb=" N   LEU E 498 " --> pdb=" O   GLY E 494 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 508 through 520
      removed outlier: 3.666A  pdb=" N   LEU E 512 " --> pdb=" O   THR E 508 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 532 through 539
    Processing helix  chain 'E' and resid 540 through 545
      removed outlier: 4.234A  pdb=" N   PHE E 544 " --> pdb=" O   ILE E 541 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU E 545 " --> pdb=" O   LEU E 542 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 561 through 568
      removed outlier: 3.699A  pdb=" N   VAL E 565 " --> pdb=" O   LEU E 561 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 581 through 585
      removed outlier: 4.243A  pdb=" N   VAL E 584 " --> pdb=" O   ASP E 581 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 588 through 594
    Processing helix  chain 'E' and resid 608 through 616
      removed outlier: 3.682A  pdb=" N   ASN E 614 " --> pdb=" O   GLN E 610 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 618 through 623
    Processing helix  chain 'E' and resid 648 through 659
    Processing helix  chain 'E' and resid 660 through 670
      removed outlier: 3.695A  pdb=" N   SER E 670 " --> pdb=" O   ASN E 666 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 680 through 702
      removed outlier: 3.602A  pdb=" N   SER E 700 " --> pdb=" O   THR E 696 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ASN E 702 " --> pdb=" O   GLN E 698 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 705 through 721
      removed outlier: 5.181A  pdb=" N   GLN E 711 " --> pdb=" O   VAL E 707 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   SER E 714 " --> pdb=" O   THR E 710 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLU E 715 " --> pdb=" O   GLN E 711 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 729 through 740
      removed outlier: 3.630A  pdb=" N   LEU E 740 " --> pdb=" O   ILE E 736 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 750 through 761
    Processing helix  chain 'E' and resid 768 through 787
    Processing helix  chain 'E' and resid 801 through 808
      removed outlier: 4.047A  pdb=" N   GLY E 805 " --> pdb=" O   SER E 801 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 820 through 826
    Processing helix  chain 'E' and resid 835 through 841
    Processing helix  chain 'E' and resid 842 through 845
    Processing helix  chain 'E' and resid 846 through 857
    Processing helix  chain 'E' and resid 861 through 871
    Processing helix  chain 'E' and resid 878 through 895
    Processing helix  chain 'E' and resid 912 through 920
      removed outlier: 3.518A  pdb=" N   TYR E 920 " --> pdb=" O   PHE E 916 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 928 through 933
    Processing helix  chain 'E' and resid 955 through 960
    Processing helix  chain 'E' and resid 969 through 974
    Processing helix  chain 'E' and resid 980 through 991
      removed outlier: 4.124A  pdb=" N   LEU E 984 " --> pdb=" O   VAL E 980 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 993 through 1003
      removed outlier: 3.714A  pdb=" N   LEU E 997 " --> pdb=" O   ASP E 993 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152
      removed outlier: 6.247A  pdb=" N   SER A 150 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   LYS A 169 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   ILE A 152 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   THR A 131 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   LEU A  42 " --> pdb=" O   HIS A 128 " (cutoff:3.500A)
      removed outlier: 8.424A  pdb=" N   ILE A 130 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   PHE A  44 " --> pdb=" O   ILE A 130 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   VAL A  43 " --> pdb=" O   VAL A 214 " (cutoff:3.500A)
      removed outlier: 8.047A  pdb=" N   ILE A 216 " --> pdb=" O   VAL A  43 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   PHE A  45 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 244 through 247
    Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 340
      removed outlier: 3.543A  pdb=" N   VAL A 347 " --> pdb=" O   HIS A 339 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 150 through 152
      removed outlier: 6.956A  pdb=" N   VAL E 129 " --> pdb=" O   LEU E 168 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   HIS E 128 " --> pdb=" O   LEU E  42 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE E 130 " --> pdb=" O   PHE E  44 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   VAL E  43 " --> pdb=" O   VAL E 214 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   ILE E 216 " --> pdb=" O   VAL E  43 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   PHE E  45 " --> pdb=" O   ILE E 216 " (cutoff:3.500A)

    722 hydrogen bonds defined for protein.
    2088 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: 2.96

  Time building geometry restraints manager: 2.11 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: 5184
        1.34 -     1.46: 2852
        1.46 -     1.58: 8793
        1.58 -     1.70: 0
        1.70 -     1.82: 108
  Bond restraints: 16937
  Sorted by residual:
  bond pdb=" N   LEU A 551 "
       pdb=" CA  LEU A 551 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 9.10e-03 1.21e+04 1.08e+01
  bond pdb=" N   LYS A 857 "
       pdb=" CA  LYS A 857 "
    ideal  model  delta    sigma   weight residual
    1.454  1.492 -0.039 1.23e-02 6.61e+03 9.81e+00
  bond pdb=" N   GLN E 236 "
       pdb=" CA  GLN E 236 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.21e-02 6.83e+03 7.44e+00
  bond pdb=" N   SER A 858 "
       pdb=" CA  SER A 858 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 1.32e-02 5.74e+03 7.09e+00
  bond pdb=" N   GLN A 549 "
       pdb=" CA  GLN A 549 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.21e-02 6.83e+03 7.01e+00
  ... (remaining 16932 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 22341
        1.83 -     3.67: 397
        3.67 -     5.50: 58
        5.50 -     7.33: 13
        7.33 -     9.16: 2
  Bond angle restraints: 22811
  Sorted by residual:
  angle pdb=" N   VAL E 980 "
        pdb=" CA  VAL E 980 "
        pdb=" C   VAL E 980 "
      ideal   model   delta    sigma   weight residual
     113.53  107.32    6.21 9.80e-01 1.04e+00 4.01e+01
  angle pdb=" N   HIS E 810 "
        pdb=" CA  HIS E 810 "
        pdb=" C   HIS E 810 "
      ideal   model   delta    sigma   weight residual
     113.38  107.10    6.28 1.23e+00 6.61e-01 2.61e+01
  angle pdb=" N   PHE E 811 "
        pdb=" CA  PHE E 811 "
        pdb=" C   PHE E 811 "
      ideal   model   delta    sigma   weight residual
     113.88  108.16    5.72 1.23e+00 6.61e-01 2.16e+01
  angle pdb=" N   GLU A 860 "
        pdb=" CA  GLU A 860 "
        pdb=" C   GLU A 860 "
      ideal   model   delta    sigma   weight residual
     113.97  109.05    4.92 1.28e+00 6.10e-01 1.48e+01
  angle pdb=" N   ALA A 623 "
        pdb=" CA  ALA A 623 "
        pdb=" C   ALA A 623 "
      ideal   model   delta    sigma   weight residual
     113.21  108.94    4.27 1.15e+00 7.56e-01 1.38e+01
  ... (remaining 22806 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.52: 8913
       16.52 -    33.04: 946
       33.04 -    49.56: 162
       49.56 -    66.08: 64
       66.08 -    82.60: 14
  Dihedral angle restraints: 10099
    sinusoidal: 4205
      harmonic: 5894
  Sorted by residual:
  dihedral pdb=" CA  SER E 317 "
           pdb=" C   SER E 317 "
           pdb=" N   PRO E 318 "
           pdb=" CA  PRO E 318 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.63   25.37     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" CA  GLU E 648 "
           pdb=" C   GLU E 648 "
           pdb=" N   TYR E 649 "
           pdb=" CA  TYR E 649 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.03  -19.97     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  TYR A 596 "
           pdb=" C   TYR A 596 "
           pdb=" N   GLU A 597 "
           pdb=" CA  GLU A 597 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.28  -16.72     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 10096 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1793
       0.043 -    0.086: 497
       0.086 -    0.130: 112
       0.130 -    0.173: 9
       0.173 -    0.216: 5
  Chirality restraints: 2416
  Sorted by residual:
  chirality pdb=" CB  ILE A 524 "
            pdb=" CA  ILE A 524 "
            pdb=" CG1 ILE A 524 "
            pdb=" CG2 ILE A 524 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  VAL A 859 "
            pdb=" N   VAL A 859 "
            pdb=" C   VAL A 859 "
            pdb=" CB  VAL A 859 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CA  LEU A 551 "
            pdb=" N   LEU A 551 "
            pdb=" C   LEU A 551 "
            pdb=" CB  LEU A 551 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 2413 not shown)

  Planarity restraints: 2914
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 247 "   -0.453 9.50e-02 1.11e+02   2.03e-01 2.54e+01
        pdb=" NE  ARG A 247 "    0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 247 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 247 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 247 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 601 "    0.018 2.00e-02 2.50e+03   1.62e-02 6.59e+00
        pdb=" CG  TRP A 601 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 601 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 601 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 601 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 601 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 601 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 601 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 601 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 601 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 855 "    0.010 2.00e-02 2.50e+03   2.02e-02 4.08e+00
        pdb=" C   SER A 855 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   SER A 855 "    0.013 2.00e-02 2.50e+03
        pdb=" N   PHE A 856 "    0.012 2.00e-02 2.50e+03
  ... (remaining 2911 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.26: 12
        2.26 -     2.92: 7021
        2.92 -     3.58: 26056
        3.58 -     4.24: 37806
        4.24 -     4.90: 61828
  Nonbonded interactions: 132723
  Sorted by model distance:
  nonbonded pdb=" O   ASN E 230 "
            pdb=" CD  LYS E 234 "
     model   vdw
     1.594 3.440
  nonbonded pdb=" O   ASN E 230 "
            pdb=" CE  LYS E 234 "
     model   vdw
     1.937 3.440
  nonbonded pdb=" O   ASN E 230 "
            pdb=" CG  LYS E 234 "
     model   vdw
     1.951 3.440
  nonbonded pdb=" OH  TYR E 218 "
            pdb=" ND2 ASN E 224 "
     model   vdw
     2.160 3.120
  nonbonded pdb=" NH2 ARG A 802 "
            pdb=" O   ARG A 870 "
     model   vdw
     2.188 3.120
  ... (remaining 132718 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 15 through 637 or resid 642 through 895 or resid 897 throu \ 
gh 1005))
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             12.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     17.220
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.030
  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:1.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
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      :  0.003   0.039  16937  Z= 0.169
  Angle     :  0.585   9.164  22811  Z= 0.342
  Chirality :  0.042   0.216   2416
  Planarity :  0.005   0.203   2914
  Dihedral  : 14.266  82.603   6315
  Min Nonbonded Distance : 1.594

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.44 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.19), residues: 1980
  helix:  0.49 (0.16), residues: 1042
  sheet: -1.46 (0.62), residues: 75
  loop : -1.37 (0.20), residues: 863

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 566 
 TYR   0.020   0.001   TYR A 596 
 PHE   0.028   0.001   PHE E 907 
 TRP   0.044   0.002   TRP A 601 
 HIS   0.005   0.001   HIS E 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (16937)
  covalent geometry    : angle       0.58479 (22811)
  hydrogen bonds       : bond        0.18196 (  722)
  hydrogen bonds       : angle       6.45719 ( 2088)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 0.717 
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: A  204 MET cc_start: 0.8068 (tmm) cc_final: 0.7835 (tmm)
REVERT: A  419 ASP cc_start: 0.8682 (p0) cc_final: 0.8407 (p0)
REVERT: A  523 ASN cc_start: 0.8627 (t0) cc_final: 0.8303 (t0)
REVERT: A  608 PHE cc_start: 0.7693 (p90) cc_final: 0.7318 (p90)
REVERT: E  544 PHE cc_start: 0.8882 (m-80) cc_final: 0.8166 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1397
  time to fit residues: 30.8816
Evaluate side-chains
  103 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 194 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    0.0060
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
A 895 ASN
A 910 ASN
A 973 ASN
A 975 HIS
A 979 HIS
** E 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 814 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.062978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.051123 restraints weight = 109991.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.052324 restraints weight = 75686.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.053149 restraints weight = 58238.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.053759 restraints weight = 48310.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.054140 restraints weight = 42019.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.1021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  16937  Z= 0.114
  Angle     :  0.516   5.970  22811  Z= 0.279
  Chirality :  0.040   0.171   2416
  Planarity :  0.003   0.049   2914
  Dihedral  :  4.071  25.414   2189
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.19), residues: 1980
  helix:  0.67 (0.16), residues: 1064
  sheet: -1.30 (0.62), residues: 77
  loop : -1.37 (0.21), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 566 
 TYR   0.018   0.001   TYR A 596 
 PHE   0.020   0.001   PHE E 907 
 TRP   0.026   0.001   TRP A 601 
 HIS   0.005   0.001   HIS E 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (16937)
  covalent geometry    : angle       0.51588 (22811)
  hydrogen bonds       : bond        0.04201 (  722)
  hydrogen bonds       : angle       4.74292 ( 2088)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  208 ILE cc_start: 0.9358 (mm) cc_final: 0.9152 (mm)
REVERT: A  419 ASP cc_start: 0.8513 (p0) cc_final: 0.8167 (p0)
REVERT: A  523 ASN cc_start: 0.8748 (t0) cc_final: 0.8524 (t0)
REVERT: A  601 TRP cc_start: 0.6957 (t60) cc_final: 0.6429 (t60)
REVERT: A  608 PHE cc_start: 0.7743 (p90) cc_final: 0.7312 (p90)
REVERT: E  421 MET cc_start: 0.8350 (tpp) cc_final: 0.8137 (tpp)
REVERT: E  525 ASP cc_start: 0.8778 (m-30) cc_final: 0.8485 (p0)
REVERT: E  544 PHE cc_start: 0.8833 (m-80) cc_final: 0.8389 (m-10)
REVERT: E  827 LEU cc_start: 0.8222 (mt) cc_final: 0.7669 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1391
  time to fit residues: 30.9771
Evaluate side-chains
  97 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 154 optimal weight:    3.9990
   chunk 49 optimal weight:   10.0000
   chunk 140 optimal weight:    3.9990
   chunk 117 optimal weight:    0.0470
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 142 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    1.9884

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

Flipped N/Q/H residues before XYZ refinement:
A 881 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.060255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.048583 restraints weight = 114639.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.049722 restraints weight = 79892.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.050523 restraints weight = 62002.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.051086 restraints weight = 51633.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.051452 restraints weight = 45149.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  16937  Z= 0.212
  Angle     :  0.611   8.866  22811  Z= 0.329
  Chirality :  0.042   0.199   2416
  Planarity :  0.004   0.061   2914
  Dihedral  :  4.423  22.379   2189
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.61 (0.19), residues: 1980
  helix:  0.48 (0.16), residues: 1073
  sheet: -1.69 (0.59), residues: 77
  loop : -1.41 (0.21), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 613 
 TYR   0.020   0.002   TYR A 596 
 PHE   0.021   0.002   PHE A 594 
 TRP   0.020   0.002   TRP A 601 
 HIS   0.007   0.001   HIS E 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (16937)
  covalent geometry    : angle       0.61113 (22811)
  hydrogen bonds       : bond        0.04577 (  722)
  hydrogen bonds       : angle       4.95190 ( 2088)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.8311 (tmm) cc_final: 0.8087 (tmm)
REVERT: A  523 ASN cc_start: 0.8880 (t0) cc_final: 0.8642 (t0)
REVERT: A  578 MET cc_start: 0.1786 (ptt) cc_final: 0.1565 (ptp)
REVERT: A  608 PHE cc_start: 0.7942 (p90) cc_final: 0.7479 (p90)
REVERT: E  227 MET cc_start: 0.9163 (ptp) cc_final: 0.8921 (ptt)
REVERT: E  304 LYS cc_start: 0.6514 (pttp) cc_final: 0.6104 (pttp)
REVERT: E  421 MET cc_start: 0.8415 (tpp) cc_final: 0.8207 (tpp)
REVERT: E  837 PHE cc_start: 0.8699 (t80) cc_final: 0.8351 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1205
  time to fit residues: 25.4898
Evaluate side-chains
  95 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 115 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 137 optimal weight:    0.7980
   chunk 175 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 179 optimal weight:    0.8980
   chunk 193 optimal weight:    0.9990
   chunk 117 optimal weight:    0.7980
   chunk 116 optimal weight:    3.9990
   chunk 161 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.061252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.049633 restraints weight = 112181.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.050788 restraints weight = 78052.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.051601 restraints weight = 60446.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.052181 restraints weight = 50221.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.052585 restraints weight = 43818.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  16937  Z= 0.115
  Angle     :  0.527   6.130  22811  Z= 0.281
  Chirality :  0.040   0.232   2416
  Planarity :  0.003   0.043   2914
  Dihedral  :  4.284  24.771   2189
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  3.23 %
    Favored  : 96.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.19), residues: 1980
  helix:  0.59 (0.16), residues: 1074
  sheet: -1.60 (0.60), residues: 78
  loop : -1.40 (0.21), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 165 
 TYR   0.020   0.001   TYR A 596 
 PHE   0.016   0.001   PHE E 877 
 TRP   0.017   0.001   TRP A 601 
 HIS   0.003   0.001   HIS E 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (16937)
  covalent geometry    : angle       0.52746 (22811)
  hydrogen bonds       : bond        0.03739 (  722)
  hydrogen bonds       : angle       4.51169 ( 2088)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  523 ASN cc_start: 0.8816 (t0) cc_final: 0.8598 (t0)
REVERT: A  531 MET cc_start: 0.8202 (ttt) cc_final: 0.7838 (ttt)
REVERT: A  608 PHE cc_start: 0.7926 (p90) cc_final: 0.7423 (p90)
REVERT: E  227 MET cc_start: 0.9042 (ptp) cc_final: 0.8681 (ptp)
REVERT: E  421 MET cc_start: 0.8442 (tpp) cc_final: 0.8199 (tpp)
REVERT: E  525 ASP cc_start: 0.8823 (m-30) cc_final: 0.8467 (p0)
REVERT: E  589 TYR cc_start: 0.7348 (m-80) cc_final: 0.7053 (m-80)
REVERT: E  837 PHE cc_start: 0.8576 (t80) cc_final: 0.8347 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 138
  average time/residue: 0.1218
  time to fit residues: 26.1012
Evaluate side-chains
  98 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 165 optimal weight:    5.9990
   chunk 138 optimal weight:    7.9990
   chunk 100 optimal weight:    0.0980
   chunk 192 optimal weight:    0.9990
   chunk 18 optimal weight:    0.2980
   chunk 83 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 16 optimal weight:    0.4980
   chunk 49 optimal weight:    7.9990
   chunk 109 optimal weight:    1.9990
   overall best weight:    0.5782

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

Flipped N/Q/H residues before XYZ refinement:
E 415 HIS
E 548 ASN
** E 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.061765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.049886 restraints weight = 112041.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.051143 restraints weight = 75950.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.052008 restraints weight = 57780.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.052566 restraints weight = 47504.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.053022 restraints weight = 41366.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  16937  Z= 0.107
  Angle     :  0.523   7.024  22811  Z= 0.277
  Chirality :  0.040   0.189   2416
  Planarity :  0.003   0.036   2914
  Dihedral  :  4.213  25.286   2189
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.19), residues: 1980
  helix:  0.67 (0.16), residues: 1071
  sheet: -1.40 (0.61), residues: 78
  loop : -1.38 (0.21), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 165 
 TYR   0.021   0.001   TYR E 611 
 PHE   0.019   0.001   PHE A 594 
 TRP   0.011   0.001   TRP E 231 
 HIS   0.003   0.001   HIS E 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (16937)
  covalent geometry    : angle       0.52331 (22811)
  hydrogen bonds       : bond        0.03551 (  722)
  hydrogen bonds       : angle       4.43715 ( 2088)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  523 ASN cc_start: 0.8790 (t0) cc_final: 0.8575 (t0)
REVERT: A  608 PHE cc_start: 0.7945 (p90) cc_final: 0.7437 (p90)
REVERT: E  227 MET cc_start: 0.9190 (ptp) cc_final: 0.8949 (ptt)
REVERT: E  525 ASP cc_start: 0.8835 (m-30) cc_final: 0.8505 (p0)
REVERT: E  589 TYR cc_start: 0.7464 (m-80) cc_final: 0.7106 (m-80)
REVERT: E  671 CYS cc_start: 0.8644 (t) cc_final: 0.8220 (t)
REVERT: E  837 PHE cc_start: 0.8566 (t80) cc_final: 0.8347 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1225
  time to fit residues: 26.6152
Evaluate side-chains
  100 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 167 optimal weight:    0.9980
   chunk 177 optimal weight:    0.0270
   chunk 187 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 144 optimal weight:    0.8980
   chunk 178 optimal weight:    4.9990
   chunk 138 optimal weight:    8.9990
   chunk 44 optimal weight:    2.9990
   chunk 157 optimal weight:    1.9990
   chunk 175 optimal weight:    0.6980
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.061631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.049981 restraints weight = 111563.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.051196 restraints weight = 76623.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.052025 restraints weight = 58589.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.052625 restraints weight = 48387.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.053044 restraints weight = 41971.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  16937  Z= 0.110
  Angle     :  0.530   8.198  22811  Z= 0.279
  Chirality :  0.040   0.166   2416
  Planarity :  0.003   0.036   2914
  Dihedral  :  4.190  25.005   2189
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.42 (0.19), residues: 1980
  helix:  0.66 (0.16), residues: 1067
  sheet: -1.75 (0.57), residues: 90
  loop : -1.31 (0.21), residues: 823

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 760 
 TYR   0.020   0.001   TYR E 611 
 PHE   0.017   0.001   PHE A 605 
 TRP   0.045   0.002   TRP A 601 
 HIS   0.004   0.001   HIS A 881 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (16937)
  covalent geometry    : angle       0.52969 (22811)
  hydrogen bonds       : bond        0.03520 (  722)
  hydrogen bonds       : angle       4.39152 ( 2088)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.622 
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: A  208 ILE cc_start: 0.9382 (mm) cc_final: 0.9157 (mm)
REVERT: A  419 ASP cc_start: 0.8379 (p0) cc_final: 0.8054 (p0)
REVERT: A  523 ASN cc_start: 0.8714 (t0) cc_final: 0.8477 (t0)
REVERT: A  608 PHE cc_start: 0.7899 (p90) cc_final: 0.7388 (p90)
REVERT: E  304 LYS cc_start: 0.6092 (pttp) cc_final: 0.5505 (pttp)
REVERT: E  525 ASP cc_start: 0.8833 (m-30) cc_final: 0.8512 (p0)
REVERT: E  589 TYR cc_start: 0.7409 (m-80) cc_final: 0.7065 (m-80)
REVERT: E  671 CYS cc_start: 0.8639 (t) cc_final: 0.8227 (t)
REVERT: E  837 PHE cc_start: 0.8506 (t80) cc_final: 0.8223 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1230
  time to fit residues: 26.5927
Evaluate side-chains
  105 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 167 optimal weight:    0.3980
   chunk 55 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   chunk 111 optimal weight:    0.7980
   chunk 106 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0980
   chunk 0 optimal weight:   10.0000
   chunk 176 optimal weight:    1.9990
   chunk 110 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.061963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.050126 restraints weight = 111866.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.051375 restraints weight = 75921.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.052246 restraints weight = 57792.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.052850 restraints weight = 47444.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.053299 restraints weight = 41033.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  16937  Z= 0.104
  Angle     :  0.525   9.144  22811  Z= 0.276
  Chirality :  0.039   0.151   2416
  Planarity :  0.003   0.036   2914
  Dihedral  :  4.149  25.434   2189
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.19), residues: 1980
  helix:  0.66 (0.16), residues: 1075
  sheet: -1.71 (0.56), residues: 90
  loop : -1.34 (0.21), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 613 
 TYR   0.022   0.001   TYR E 611 
 PHE   0.020   0.001   PHE A 605 
 TRP   0.009   0.001   TRP E 448 
 HIS   0.003   0.000   HIS A 881 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (16937)
  covalent geometry    : angle       0.52532 (22811)
  hydrogen bonds       : bond        0.03435 (  722)
  hydrogen bonds       : angle       4.31399 ( 2088)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ASP cc_start: 0.8806 (t0) cc_final: 0.8464 (t0)
REVERT: A  419 ASP cc_start: 0.8432 (p0) cc_final: 0.8112 (p0)
REVERT: A  523 ASN cc_start: 0.8723 (t0) cc_final: 0.8443 (t0)
REVERT: A  608 PHE cc_start: 0.7938 (p90) cc_final: 0.7400 (p90)
REVERT: E  227 MET cc_start: 0.9146 (ptp) cc_final: 0.8697 (ptt)
REVERT: E  304 LYS cc_start: 0.6094 (pttp) cc_final: 0.5495 (pttp)
REVERT: E  525 ASP cc_start: 0.8811 (m-30) cc_final: 0.8513 (p0)
REVERT: E  589 TYR cc_start: 0.7473 (m-80) cc_final: 0.7107 (m-80)
REVERT: E  671 CYS cc_start: 0.8757 (t) cc_final: 0.8307 (t)
REVERT: E  827 LEU cc_start: 0.8294 (mt) cc_final: 0.7707 (tp)
REVERT: E  837 PHE cc_start: 0.8522 (t80) cc_final: 0.8213 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1173
  time to fit residues: 25.7190
Evaluate side-chains
  99 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 127 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0770
   chunk 118 optimal weight:    0.7980
   chunk 112 optimal weight:    0.9980
   chunk 111 optimal weight:    5.9990
   chunk 171 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 188 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
A 666 ASN
A 961 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.063431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.051912 restraints weight = 118909.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.053085 restraints weight = 83064.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.053900 restraints weight = 64696.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.054393 restraints weight = 54183.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.054834 restraints weight = 48032.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  16937  Z= 0.111
  Angle     :  0.546  11.339  22811  Z= 0.283
  Chirality :  0.039   0.161   2416
  Planarity :  0.003   0.042   2914
  Dihedral  :  4.165  25.366   2189
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.19), residues: 1980
  helix:  0.67 (0.16), residues: 1080
  sheet: -1.69 (0.56), residues: 90
  loop : -1.33 (0.21), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E 566 
 TYR   0.020   0.001   TYR A 596 
 PHE   0.021   0.001   PHE A 605 
 TRP   0.051   0.002   TRP A 601 
 HIS   0.005   0.001   HIS A 978 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (16937)
  covalent geometry    : angle       0.54611 (22811)
  hydrogen bonds       : bond        0.03414 (  722)
  hydrogen bonds       : angle       4.32773 ( 2088)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ASP cc_start: 0.8799 (t0) cc_final: 0.8453 (t0)
REVERT: A  419 ASP cc_start: 0.8434 (p0) cc_final: 0.8113 (p0)
REVERT: A  523 ASN cc_start: 0.8766 (t0) cc_final: 0.8502 (t0)
REVERT: A  608 PHE cc_start: 0.7956 (p90) cc_final: 0.7421 (p90)
REVERT: E  227 MET cc_start: 0.9211 (ptp) cc_final: 0.8540 (ptt)
REVERT: E  304 LYS cc_start: 0.6244 (pttp) cc_final: 0.5690 (pttp)
REVERT: E  421 MET cc_start: 0.8500 (tpp) cc_final: 0.8206 (tpp)
REVERT: E  525 ASP cc_start: 0.8820 (m-30) cc_final: 0.8520 (p0)
REVERT: E  589 TYR cc_start: 0.7579 (m-80) cc_final: 0.7216 (m-80)
REVERT: E  613 ARG cc_start: 0.8347 (mmp80) cc_final: 0.8059 (mmp80)
REVERT: E  647 MET cc_start: 0.8839 (mpp) cc_final: 0.8573 (mpp)
REVERT: E  827 LEU cc_start: 0.8350 (mt) cc_final: 0.7753 (tp)
REVERT: E  837 PHE cc_start: 0.8561 (t80) cc_final: 0.8199 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1135
  time to fit residues: 24.7908
Evaluate side-chains
  100 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 183 optimal weight:    7.9990
   chunk 147 optimal weight:    0.9980
   chunk 127 optimal weight:    1.9990
   chunk 85 optimal weight:    0.3980
   chunk 4 optimal weight:    4.9990
   chunk 62 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 178 optimal weight:    0.3980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** E 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.063558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.052005 restraints weight = 118997.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.053171 restraints weight = 83096.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.054000 restraints weight = 64908.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.054556 restraints weight = 54326.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.054951 restraints weight = 47856.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  16937  Z= 0.109
  Angle     :  0.548  10.190  22811  Z= 0.284
  Chirality :  0.040   0.295   2416
  Planarity :  0.003   0.045   2914
  Dihedral  :  4.148  25.765   2189
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    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: -0.37 (0.19), residues: 1980
  helix:  0.69 (0.16), residues: 1079
  sheet: -1.64 (0.57), residues: 90
  loop : -1.33 (0.21), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 566 
 TYR   0.020   0.001   TYR E 611 
 PHE   0.022   0.001   PHE A 605 
 TRP   0.046   0.001   TRP A 601 
 HIS   0.003   0.001   HIS A 978 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (16937)
  covalent geometry    : angle       0.54839 (22811)
  hydrogen bonds       : bond        0.03403 (  722)
  hydrogen bonds       : angle       4.30678 ( 2088)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ASP cc_start: 0.8695 (t0) cc_final: 0.8379 (t0)
REVERT: A  419 ASP cc_start: 0.8339 (p0) cc_final: 0.8011 (p0)
REVERT: A  523 ASN cc_start: 0.8718 (t0) cc_final: 0.8469 (t0)
REVERT: A  608 PHE cc_start: 0.7922 (p90) cc_final: 0.7357 (p90)
REVERT: A  912 TYR cc_start: 0.7336 (m-10) cc_final: 0.5994 (m-80)
REVERT: E   22 LEU cc_start: 0.7993 (tt) cc_final: 0.7657 (mt)
REVERT: E  227 MET cc_start: 0.9155 (ptp) cc_final: 0.8424 (ptt)
REVERT: E  304 LYS cc_start: 0.6002 (pttp) cc_final: 0.5424 (pttp)
REVERT: E  421 MET cc_start: 0.8460 (tpp) cc_final: 0.8187 (tpp)
REVERT: E  519 MET cc_start: 0.9160 (mmm) cc_final: 0.8939 (mmt)
REVERT: E  525 ASP cc_start: 0.8795 (m-30) cc_final: 0.8552 (p0)
REVERT: E  558 LEU cc_start: 0.8487 (mm) cc_final: 0.8261 (mp)
REVERT: E  589 TYR cc_start: 0.7519 (m-80) cc_final: 0.7157 (m-80)
REVERT: E  827 LEU cc_start: 0.8327 (mt) cc_final: 0.7740 (tp)
REVERT: E  837 PHE cc_start: 0.8450 (t80) cc_final: 0.8101 (t80)
REVERT: E  969 LYS cc_start: 0.6434 (mttt) cc_final: 0.6007 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1168
  time to fit residues: 25.3988
Evaluate side-chains
  102 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 78 optimal weight:    0.0570
   chunk 0 optimal weight:   10.0000
   chunk 197 optimal weight:    0.0470
   chunk 150 optimal weight:    0.8980
   chunk 102 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 124 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
E 297 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.063007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.049831 restraints weight = 111245.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.051066 restraints weight = 78171.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.051927 restraints weight = 61103.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.052512 restraints weight = 51176.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.052960 restraints weight = 45188.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  16937  Z= 0.105
  Angle     :  0.553  10.459  22811  Z= 0.285
  Chirality :  0.040   0.274   2416
  Planarity :  0.003   0.047   2914
  Dihedral  :  4.135  25.973   2189
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.19), residues: 1980
  helix:  0.69 (0.16), residues: 1080
  sheet: -1.65 (0.56), residues: 90
  loop : -1.32 (0.21), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 566 
 TYR   0.019   0.001   TYR E 725 
 PHE   0.023   0.001   PHE A 605 
 TRP   0.047   0.001   TRP A 601 
 HIS   0.003   0.001   HIS A 978 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (16937)
  covalent geometry    : angle       0.55295 (22811)
  hydrogen bonds       : bond        0.03332 (  722)
  hydrogen bonds       : angle       4.26941 ( 2088)

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ASP cc_start: 0.8816 (t0) cc_final: 0.8445 (t0)
REVERT: A  419 ASP cc_start: 0.8552 (p0) cc_final: 0.8267 (p0)
REVERT: A  523 ASN cc_start: 0.8757 (t0) cc_final: 0.8509 (t0)
REVERT: A  608 PHE cc_start: 0.7885 (p90) cc_final: 0.7418 (p90)
REVERT: E   22 LEU cc_start: 0.8008 (tt) cc_final: 0.7564 (mt)
REVERT: E  227 MET cc_start: 0.9192 (ptp) cc_final: 0.8787 (ptt)
REVERT: E  304 LYS cc_start: 0.6150 (pttp) cc_final: 0.5551 (pttp)
REVERT: E  421 MET cc_start: 0.8588 (tpp) cc_final: 0.8316 (tpp)
REVERT: E  519 MET cc_start: 0.9205 (mmm) cc_final: 0.8891 (mmt)
REVERT: E  544 PHE cc_start: 0.8574 (m-10) cc_final: 0.8140 (m-80)
REVERT: E  558 LEU cc_start: 0.8446 (mm) cc_final: 0.8232 (mp)
REVERT: E  589 TYR cc_start: 0.7492 (m-80) cc_final: 0.7134 (m-80)
REVERT: E  827 LEU cc_start: 0.8490 (mt) cc_final: 0.7893 (tp)
REVERT: E  837 PHE cc_start: 0.8602 (t80) cc_final: 0.8262 (t80)
REVERT: E  969 LYS cc_start: 0.6479 (mttt) cc_final: 0.6069 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1336
  time to fit residues: 28.8446
Evaluate side-chains
  97 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 13 optimal weight:    0.0980
   chunk 101 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0770
   chunk 26 optimal weight:    0.9990
   chunk 150 optimal weight:    0.6980
   chunk 113 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 109 optimal weight:    0.3980
   chunk 9 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.3738

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

Flipped N/Q/H residues before XYZ refinement:
** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.064096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.052559 restraints weight = 118365.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.053728 restraints weight = 82542.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.054553 restraints weight = 64530.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.055117 restraints weight = 54036.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.055490 restraints weight = 47619.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  16937  Z= 0.099
  Angle     :  0.549  11.729  22811  Z= 0.281
  Chirality :  0.040   0.265   2416
  Planarity :  0.003   0.049   2914
  Dihedral  :  4.063  26.124   2189
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.34 (0.19), residues: 1980
  helix:  0.72 (0.16), residues: 1086
  sheet: -1.58 (0.56), residues: 90
  loop : -1.34 (0.21), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 566 
 TYR   0.028   0.001   TYR E 721 
 PHE   0.023   0.001   PHE A 605 
 TRP   0.045   0.001   TRP A 601 
 HIS   0.009   0.001   HIS E 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 (16937)
  covalent geometry    : angle       0.54876 (22811)
  hydrogen bonds       : bond        0.03207 (  722)
  hydrogen bonds       : angle       4.22643 ( 2088)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2392.68 seconds
wall clock time: 42 minutes 39.42 seconds (2559.42 seconds total)