Starting phenix.real_space_refine
on Tue Jan 21 10:48:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wkx_37610/01_2025/8wkx_37610.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wkx_37610/01_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_37610/01_2025/8wkx_37610.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wkx_37610/01_2025/8wkx_37610.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wkx_37610/01_2025/8wkx_37610.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wkx_37610/01_2025/8wkx_37610.cif"
  }
  resolution = 4.15
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 11.48, per 1000 atoms: 0.69
  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: 4.23
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  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: 1.74
  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: 5.44

  Time building geometry restraints manager: 4.79 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:             9.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.650
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     39.560
  Find NCS groups from input model:        0.720
  Set up NCS constraints:                  0.080
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.270
-------------------------------------------------------------------------------
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= 0.176
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (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
 TRP   0.044   0.002   TRP A 601 
 HIS   0.005   0.001   HIS E 339 
 PHE   0.028   0.001   PHE E 907 
 TYR   0.020   0.001   TYR A 596 
 ARG   0.006   0.000   ARG E 566 

*********************** 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  : 2.247 
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: 0.7837 (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: 0.8302 (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: 0.3257
  time to fit residues: 71.7221
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  : 2.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 167 optimal weight:    2.9990
   chunk 150 optimal weight:    4.9990
   chunk 83 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 101 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 155 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 115 optimal weight:    3.9990
   chunk 179 optimal weight:    0.7980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 814 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.062447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.050656 restraints weight = 111054.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.051833 restraints weight = 77105.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.052649 restraints weight = 59593.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  16937  Z= 0.177
  Angle     :  0.524   5.920  22811  Z= 0.284
  Chirality :  0.040   0.171   2416
  Planarity :  0.003   0.051   2914
  Dihedral  :  4.104  24.820   2189
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.19), residues: 1980
  helix:  0.66 (0.16), residues: 1065
  sheet: -1.44 (0.61), residues: 78
  loop : -1.35 (0.21), residues: 837

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 601 
 HIS   0.005   0.001   HIS E 339 
 PHE   0.020   0.001   PHE E 907 
 TYR   0.017   0.001   TYR A 596 
 ARG   0.006   0.000   ARG E 566 

*********************** 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
  141 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 2.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.8191 (tmm) cc_final: 0.7985 (tmm)
REVERT: A  419 ASP cc_start: 0.8589 (p0) cc_final: 0.8263 (p0)
REVERT: A  523 ASN cc_start: 0.8776 (t0) cc_final: 0.8562 (t0)
REVERT: A  601 TRP cc_start: 0.7004 (t60) cc_final: 0.6358 (t60)
REVERT: A  608 PHE cc_start: 0.7784 (p90) cc_final: 0.7342 (p90)
REVERT: E  421 MET cc_start: 0.8358 (tpp) cc_final: 0.8149 (tpp)
REVERT: E  525 ASP cc_start: 0.8846 (m-30) cc_final: 0.8535 (p0)
REVERT: E  544 PHE cc_start: 0.8920 (m-80) cc_final: 0.8420 (m-10)
REVERT: E  827 LEU cc_start: 0.8295 (mt) cc_final: 0.7755 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.2988
  time to fit residues: 65.2703
Evaluate side-chains
  96 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 1.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 143 optimal weight:    1.9990
   chunk 104 optimal weight:    0.0270
   chunk 35 optimal weight:    0.8980
   chunk 110 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 185 optimal weight:    0.0970
   chunk 184 optimal weight:    0.9980
   chunk 137 optimal weight:    0.9990
   chunk 158 optimal weight:    2.9990
   overall best weight:    0.6036

-------------------------------------------------------------------------------
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 = 0.3578 r_free = 0.3578 target = 0.064555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.053025 restraints weight = 118454.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.054201 restraints weight = 82504.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.055002 restraints weight = 64169.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  16937  Z= 0.147
  Angle     :  0.516   5.948  22811  Z= 0.274
  Chirality :  0.040   0.211   2416
  Planarity :  0.003   0.076   2914
  Dihedral  :  4.094  24.510   2189
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.19), residues: 1980
  helix:  0.61 (0.16), residues: 1068
  sheet: -1.29 (0.61), residues: 77
  loop : -1.41 (0.21), residues: 835

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 601 
 HIS   0.004   0.001   HIS E 339 
 PHE   0.019   0.001   PHE A 594 
 TYR   0.020   0.001   TYR A 596 
 ARG   0.005   0.000   ARG A 760 

*********************** 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
  144 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  208 ILE cc_start: 0.9327 (mm) cc_final: 0.9105 (mm)
REVERT: A  333 VAL cc_start: 0.9484 (t) cc_final: 0.9202 (t)
REVERT: A  419 ASP cc_start: 0.8421 (p0) cc_final: 0.8030 (p0)
REVERT: A  523 ASN cc_start: 0.8766 (t0) cc_final: 0.8539 (t0)
REVERT: A  608 PHE cc_start: 0.7740 (p90) cc_final: 0.7288 (p90)
REVERT: E  421 MET cc_start: 0.8314 (tpp) cc_final: 0.8080 (tpp)
REVERT: E  525 ASP cc_start: 0.8803 (m-30) cc_final: 0.8487 (p0)
REVERT: E  544 PHE cc_start: 0.8898 (m-80) cc_final: 0.8309 (m-10)
REVERT: E  827 LEU cc_start: 0.8201 (mt) cc_final: 0.7747 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.3058
  time to fit residues: 69.2917
Evaluate side-chains
  94 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 2.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 169 optimal weight:    0.8980
   chunk 79 optimal weight:    3.9990
   chunk 136 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 110 optimal weight:    0.9980
   chunk 173 optimal weight:    1.9990
   chunk 125 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 128 optimal weight:    0.0980
   chunk 189 optimal weight:    7.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3550 r_free = 0.3550 target = 0.063514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.051844 restraints weight = 119744.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.053044 restraints weight = 83119.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.053861 restraints weight = 64656.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16937  Z= 0.179
  Angle     :  0.522   6.634  22811  Z= 0.278
  Chirality :  0.040   0.239   2416
  Planarity :  0.003   0.046   2914
  Dihedral  :  4.107  23.550   2189
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.19), residues: 1980
  helix:  0.64 (0.16), residues: 1075
  sheet: -1.42 (0.60), residues: 78
  loop : -1.38 (0.21), residues: 827

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A 601 
 HIS   0.004   0.001   HIS A 609 
 PHE   0.019   0.001   PHE E 877 
 TYR   0.018   0.001   TYR A 596 
 ARG   0.007   0.000   ARG A 760 

*********************** 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
  135 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 2.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  419 ASP cc_start: 0.8350 (p0) cc_final: 0.7985 (p0)
REVERT: A  523 ASN cc_start: 0.8802 (t0) cc_final: 0.8581 (t0)
REVERT: A  531 MET cc_start: 0.8250 (ttt) cc_final: 0.7842 (ttt)
REVERT: A  578 MET cc_start: 0.1859 (ptt) cc_final: 0.1582 (ptp)
REVERT: A  608 PHE cc_start: 0.7880 (p90) cc_final: 0.7376 (p90)
REVERT: E  223 TYR cc_start: 0.7842 (t80) cc_final: 0.7357 (t80)
REVERT: E  525 ASP cc_start: 0.8857 (m-30) cc_final: 0.8466 (p0)
REVERT: E  589 TYR cc_start: 0.7418 (m-80) cc_final: 0.7104 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2924
  time to fit residues: 62.1447
Evaluate side-chains
  94 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 1.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 93 optimal weight:    5.9990
   chunk 117 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 138 optimal weight:    7.9990
   chunk 121 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 101 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 193 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
E 415 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.062317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.050660 restraints weight = 121644.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.051845 restraints weight = 83715.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.052666 restraints weight = 64806.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  16937  Z= 0.215
  Angle     :  0.550   6.854  22811  Z= 0.295
  Chirality :  0.040   0.185   2416
  Planarity :  0.004   0.067   2914
  Dihedral  :  4.262  23.581   2189
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  2.52 %
    Favored  : 97.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.19), residues: 1980
  helix:  0.64 (0.16), residues: 1073
  sheet: -1.52 (0.64), residues: 68
  loop : -1.35 (0.21), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 601 
 HIS   0.004   0.001   HIS A 609 
 PHE   0.025   0.001   PHE E 916 
 TYR   0.020   0.001   TYR A 596 
 ARG   0.008   0.001   ARG E 566 

*********************** 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
  135 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 1.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  419 ASP cc_start: 0.8483 (p0) cc_final: 0.8110 (p0)
REVERT: A  523 ASN cc_start: 0.8855 (t0) cc_final: 0.8630 (t0)
REVERT: A  578 MET cc_start: 0.2171 (ptt) cc_final: 0.1924 (ptp)
REVERT: A  608 PHE cc_start: 0.7999 (p90) cc_final: 0.7503 (p90)
REVERT: E  227 MET cc_start: 0.9170 (ptp) cc_final: 0.8937 (ptt)
REVERT: E  525 ASP cc_start: 0.8916 (m-30) cc_final: 0.8540 (p0)
REVERT: E  544 PHE cc_start: 0.8794 (m-80) cc_final: 0.8521 (m-80)
REVERT: E  589 TYR cc_start: 0.7449 (m-80) cc_final: 0.7154 (m-80)
REVERT: E  671 CYS cc_start: 0.8738 (t) cc_final: 0.8230 (t)
REVERT: E  837 PHE cc_start: 0.8644 (t80) cc_final: 0.8388 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 135
  average time/residue: 0.2865
  time to fit residues: 60.2986
Evaluate side-chains
  95 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 1.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 60 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 161 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 36 optimal weight:    0.4980
   chunk 179 optimal weight:    0.1980
   chunk 197 optimal weight:    0.9990
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.063423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.051902 restraints weight = 119484.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.053090 restraints weight = 83025.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.053913 restraints weight = 64546.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  16937  Z= 0.147
  Angle     :  0.528   8.588  22811  Z= 0.279
  Chirality :  0.040   0.155   2416
  Planarity :  0.003   0.037   2914
  Dihedral  :  4.169  25.073   2189
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.19), residues: 1980
  helix:  0.65 (0.16), residues: 1068
  sheet: -1.46 (0.61), residues: 78
  loop : -1.30 (0.21), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.001   TRP A 601 
 HIS   0.003   0.001   HIS E 339 
 PHE   0.017   0.001   PHE A 605 
 TYR   0.020   0.001   TYR E 611 
 ARG   0.006   0.000   ARG E 165 

*********************** 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
  139 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  419 ASP cc_start: 0.8391 (p0) cc_final: 0.7983 (p0)
REVERT: A  523 ASN cc_start: 0.8806 (t0) cc_final: 0.8587 (t0)
REVERT: A  608 PHE cc_start: 0.7824 (p90) cc_final: 0.7444 (p90)
REVERT: E  227 MET cc_start: 0.9039 (ptp) cc_final: 0.8622 (ptt)
REVERT: E  525 ASP cc_start: 0.8923 (m-30) cc_final: 0.8565 (p0)
REVERT: E  544 PHE cc_start: 0.8799 (m-80) cc_final: 0.8382 (m-10)
REVERT: E  589 TYR cc_start: 0.7508 (m-80) cc_final: 0.7187 (m-80)
REVERT: E  671 CYS cc_start: 0.8744 (t) cc_final: 0.8268 (t)
REVERT: E  827 LEU cc_start: 0.8396 (mt) cc_final: 0.7801 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.2878
  time to fit residues: 61.8715
Evaluate side-chains
  93 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 2.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 70 optimal weight:    0.1980
   chunk 4 optimal weight:    4.9990
   chunk 5 optimal weight:    0.4980
   chunk 119 optimal weight:    0.8980
   chunk 175 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 138 optimal weight:    7.9990
   chunk 103 optimal weight:    0.8980
   chunk 111 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3513 r_free = 0.3513 target = 0.061853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.050045 restraints weight = 112606.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.051291 restraints weight = 76299.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.052147 restraints weight = 58108.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  16937  Z= 0.149
  Angle     :  0.530   9.094  22811  Z= 0.281
  Chirality :  0.040   0.158   2416
  Planarity :  0.003   0.036   2914
  Dihedral  :  4.178  25.356   2189
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.19), residues: 1980
  helix:  0.68 (0.16), residues: 1068
  sheet: -1.40 (0.61), residues: 78
  loop : -1.31 (0.21), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.001   TRP A 601 
 HIS   0.007   0.001   HIS A 881 
 PHE   0.019   0.001   PHE A 605 
 TYR   0.020   0.001   TYR A 596 
 ARG   0.012   0.000   ARG E 987 

*********************** 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
  139 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 2.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.8075 (tmm) cc_final: 0.7850 (tmm)
REVERT: A  208 ILE cc_start: 0.9419 (mm) cc_final: 0.9180 (mm)
REVERT: A  419 ASP cc_start: 0.8549 (p0) cc_final: 0.8184 (p0)
REVERT: A  523 ASN cc_start: 0.8808 (t0) cc_final: 0.8561 (t0)
REVERT: A  608 PHE cc_start: 0.7894 (p90) cc_final: 0.7504 (p90)
REVERT: E  227 MET cc_start: 0.9252 (ptp) cc_final: 0.8937 (ptt)
REVERT: E  525 ASP cc_start: 0.8914 (m-30) cc_final: 0.8579 (p0)
REVERT: E  544 PHE cc_start: 0.8818 (m-80) cc_final: 0.8383 (m-10)
REVERT: E  578 MET cc_start: 0.4869 (tmm) cc_final: 0.4560 (ppp)
REVERT: E  586 LEU cc_start: 0.8265 (mp) cc_final: 0.7818 (tp)
REVERT: E  589 TYR cc_start: 0.7431 (m-80) cc_final: 0.7121 (m-80)
REVERT: E  671 CYS cc_start: 0.8756 (t) cc_final: 0.8266 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.2802
  time to fit residues: 61.4778
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  : 1.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 192 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0570
   chunk 196 optimal weight:    3.9990
   chunk 130 optimal weight:    0.6980
   chunk 82 optimal weight:    4.9990
   chunk 186 optimal weight:    0.8980
   chunk 155 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.6298

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.061925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.050105 restraints weight = 112418.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.051351 restraints weight = 76171.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.052208 restraints weight = 58040.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050  16937  Z= 0.151
  Angle     :  0.539   9.744  22811  Z= 0.281
  Chirality :  0.039   0.156   2416
  Planarity :  0.003   0.036   2914
  Dihedral  :  4.179  25.600   2189
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.19), residues: 1980
  helix:  0.70 (0.16), residues: 1071
  sheet: -1.80 (0.56), residues: 90
  loop : -1.31 (0.21), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.001   TRP A 601 
 HIS   0.005   0.001   HIS A 881 
 PHE   0.021   0.001   PHE A 605 
 TYR   0.023   0.001   TYR E 611 
 ARG   0.008   0.000   ARG E 566 

*********************** 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
  138 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 2.032 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ASP cc_start: 0.8861 (t0) cc_final: 0.8518 (t0)
REVERT: A  208 ILE cc_start: 0.9379 (mm) cc_final: 0.9137 (mm)
REVERT: A  419 ASP cc_start: 0.8542 (p0) cc_final: 0.8184 (p0)
REVERT: A  523 ASN cc_start: 0.8807 (t0) cc_final: 0.8557 (t0)
REVERT: A  608 PHE cc_start: 0.7863 (p90) cc_final: 0.7478 (p90)
REVERT: E  227 MET cc_start: 0.9214 (ptp) cc_final: 0.8298 (ptt)
REVERT: E  421 MET cc_start: 0.8366 (tpp) cc_final: 0.8029 (tpp)
REVERT: E  525 ASP cc_start: 0.8906 (m-30) cc_final: 0.8571 (p0)
REVERT: E  544 PHE cc_start: 0.8864 (m-80) cc_final: 0.8517 (m-80)
REVERT: E  586 LEU cc_start: 0.8230 (mp) cc_final: 0.7796 (tp)
REVERT: E  589 TYR cc_start: 0.7422 (m-80) cc_final: 0.7113 (m-80)
REVERT: E  613 ARG cc_start: 0.7773 (mmp80) cc_final: 0.7508 (mmp80)
REVERT: E  671 CYS cc_start: 0.8829 (t) cc_final: 0.8343 (t)
REVERT: E  827 LEU cc_start: 0.8350 (mt) cc_final: 0.7766 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.2928
  time to fit residues: 63.1731
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  : 1.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 155 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 146 optimal weight:    0.9980
   chunk 138 optimal weight:    5.9990
   chunk 108 optimal weight:    0.8980
   chunk 187 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 177 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1002 ASN
E 236 GLN
E 297 GLN
E 810 HIS
E 939 GLN
** E 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.059455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.047891 restraints weight = 115154.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.049014 restraints weight = 79952.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.049797 restraints weight = 62136.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  16937  Z= 0.287
  Angle     :  0.628   9.802  22811  Z= 0.337
  Chirality :  0.042   0.283   2416
  Planarity :  0.004   0.065   2914
  Dihedral  :  4.548  25.042   2189
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.19), residues: 1980
  helix:  0.51 (0.16), residues: 1073
  sheet: -2.08 (0.58), residues: 80
  loop : -1.27 (0.21), residues: 827

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 601 
 HIS   0.007   0.001   HIS A 658 
 PHE   0.025   0.002   PHE A 605 
 TYR   0.031   0.002   TYR E 721 
 ARG   0.008   0.001   ARG A 760 

*********************** 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
  130 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 1.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  523 ASN cc_start: 0.8840 (t0) cc_final: 0.8595 (t0)
REVERT: A  608 PHE cc_start: 0.7968 (p90) cc_final: 0.7449 (p90)
REVERT: E  227 MET cc_start: 0.9192 (ptp) cc_final: 0.8453 (ptt)
REVERT: E  421 MET cc_start: 0.8442 (tpp) cc_final: 0.8141 (tpp)
REVERT: E  448 TRP cc_start: 0.7342 (t60) cc_final: 0.6620 (t60)
REVERT: E  525 ASP cc_start: 0.8924 (m-30) cc_final: 0.8602 (p0)
REVERT: E  586 LEU cc_start: 0.8331 (mp) cc_final: 0.7919 (tp)
REVERT: E  589 TYR cc_start: 0.7480 (m-80) cc_final: 0.7145 (m-80)
REVERT: E  837 PHE cc_start: 0.8354 (t80) cc_final: 0.8078 (t80)
REVERT: E  969 LYS cc_start: 0.6428 (mttt) cc_final: 0.6082 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.2781
  time to fit residues: 56.5664
Evaluate side-chains
  92 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 1.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 128 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 153 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 167 optimal weight:    0.8980
   chunk 114 optimal weight:    0.0470
   chunk 112 optimal weight:    0.1980
   chunk 25 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.4478

-------------------------------------------------------------------------------
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**
E 548 ASN
E 979 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.062898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.051404 restraints weight = 118811.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.052559 restraints weight = 83108.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.053359 restraints weight = 65114.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  16937  Z= 0.150
  Angle     :  0.572  10.500  22811  Z= 0.299
  Chirality :  0.041   0.258   2416
  Planarity :  0.003   0.038   2914
  Dihedral  :  4.352  28.291   2189
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.19), residues: 1980
  helix:  0.63 (0.16), residues: 1079
  sheet: -1.82 (0.55), residues: 90
  loop : -1.34 (0.21), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 601 
 HIS   0.004   0.001   HIS A 881 
 PHE   0.026   0.001   PHE A 605 
 TYR   0.024   0.001   TYR E 611 
 ARG   0.009   0.000   ARG E 566 

********************** 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
  137 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 2.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ASP cc_start: 0.8796 (t0) cc_final: 0.8430 (t0)
REVERT: A  419 ASP cc_start: 0.8474 (p0) cc_final: 0.8131 (p0)
REVERT: A  608 PHE cc_start: 0.7758 (p90) cc_final: 0.7378 (p90)
REVERT: A  616 MET cc_start: 0.8250 (mmp) cc_final: 0.7981 (mmp)
REVERT: A  913 MET cc_start: 0.5710 (pmm) cc_final: 0.5494 (pmm)
REVERT: E  227 MET cc_start: 0.9147 (ptp) cc_final: 0.8754 (ptt)
REVERT: E  421 MET cc_start: 0.8397 (tpp) cc_final: 0.8051 (tpp)
REVERT: E  525 ASP cc_start: 0.8924 (m-30) cc_final: 0.8600 (p0)
REVERT: E  586 LEU cc_start: 0.8188 (mp) cc_final: 0.7808 (tp)
REVERT: E  589 TYR cc_start: 0.7421 (m-80) cc_final: 0.7111 (m-80)
REVERT: E  827 LEU cc_start: 0.8465 (mt) cc_final: 0.7896 (tp)
REVERT: E  837 PHE cc_start: 0.8173 (t80) cc_final: 0.7968 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.2882
  time to fit residues: 61.5771
Evaluate side-chains
  96 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 2.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 194 optimal weight:    0.9980
   chunk 80 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 121 optimal weight:    0.7980
   chunk 81 optimal weight:    6.9990
   chunk 49 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 186 optimal weight:    0.9980
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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**
E 548 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.060652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.049042 restraints weight = 112894.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.050172 restraints weight = 78742.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.050968 restraints weight = 61152.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  16937  Z= 0.178
  Angle     :  0.569  11.607  22811  Z= 0.299
  Chirality :  0.041   0.253   2416
  Planarity :  0.003   0.050   2914
  Dihedral  :  4.314  26.504   2189
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.19), residues: 1980
  helix:  0.67 (0.16), residues: 1082
  sheet: -1.81 (0.55), residues: 90
  loop : -1.27 (0.22), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A 601 
 HIS   0.004   0.001   HIS A 881 
 PHE   0.032   0.001   PHE A 605 
 TYR   0.029   0.001   TYR E 725 
 ARG   0.006   0.000   ARG E 613 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4436.99 seconds
wall clock time: 81 minutes 51.97 seconds (4911.97 seconds total)