Starting phenix.real_space_refine
on Mon Dec 30 20:31:38 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ztr_60470/12_2024/8ztr_60470.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ztr_60470/12_2024/8ztr_60470.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ztr_60470/12_2024/8ztr_60470.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ztr_60470/12_2024/8ztr_60470.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ztr_60470/12_2024/8ztr_60470.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ztr_60470/12_2024/8ztr_60470.cif"
  }
  resolution = 3.26
  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=   0.002 sd=   0.030
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      54      5.16       5
     C    9088      2.51       5
     N    2254      2.21       5
     O    2676      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 14072
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 702, 5887
          Classifications: {'peptide': 702}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 692}
    Chain: "B"
      Number of atoms: 5887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 702, 5887
          Classifications: {'peptide': 702}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 692}
    Chain: "E"
      Number of atoms: 1149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1149
          Classifications: {'peptide': 145}
          Link IDs: {'PTRANS': 5, 'TRANS': 139}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1149
          Classifications: {'peptide': 145}
          Link IDs: {'PTRANS': 5, 'TRANS': 139}
          Chain breaks: 1
  Time building chain proxies: 7.96, per 1000 atoms: 0.57
  Number of scatterers: 14072
  At special positions: 0
  Unit cell: (130.48, 100.656, 108.112, 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      54     16.00
     O    2676      8.00
     N    2254      7.00
     C    9088      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: 3.51
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3232

  Finding SS restraints...
    Secondary structure from input PDB file:
      84 helices and 6 sheets defined
      63.8% alpha, 8.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 304 through 317
      removed outlier: 3.543A  pdb=" N   VAL A 308 " --> pdb=" O   LYS A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 321
      removed outlier: 3.752A  pdb=" N   ALA A 321 " --> pdb=" O   PRO A 318 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 318 through 321'
    Processing helix  chain 'A' and resid 327 through 334
      removed outlier: 3.529A  pdb=" N   HIS A 332 " --> pdb=" O   ASP A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 366
    Processing helix  chain 'A' and resid 366 through 373
      removed outlier: 3.622A  pdb=" N   LEU A 373 " --> pdb=" O   GLU A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 392
    Processing helix  chain 'A' and resid 417 through 427
    Processing helix  chain 'A' and resid 431 through 445
    Processing helix  chain 'A' and resid 447 through 466
    Processing helix  chain 'A' and resid 467 through 501
      removed outlier: 5.424A  pdb=" N   LEU A 497 " --> pdb=" O   ASN A 493 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   LEU A 498 " --> pdb=" O   GLY A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 519
      removed outlier: 3.742A  pdb=" N   MET A 519 " --> pdb=" O   ILE A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 527
      removed outlier: 3.558A  pdb=" N   ASP A 526 " --> pdb=" O   ASN A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 539
    Processing helix  chain 'A' and resid 540 through 546
      removed outlier: 4.232A  pdb=" N   PHE A 544 " --> pdb=" O   ILE A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 572
      removed outlier: 3.772A  pdb=" N   VAL A 556 " --> pdb=" O   TYR A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 598
      removed outlier: 3.598A  pdb=" N   VAL A 583 " --> pdb=" O   SER A 579 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN A 598 " --> pdb=" O   PHE A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 604
      removed outlier: 3.799A  pdb=" N   VAL A 603 " --> pdb=" O   LEU A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 629
    Processing helix  chain 'A' and resid 632 through 639
    Processing helix  chain 'A' and resid 648 through 659
    Processing helix  chain 'A' and resid 660 through 671
    Processing helix  chain 'A' and resid 680 through 701
      removed outlier: 3.733A  pdb=" N   ALA A 701 " --> pdb=" O   LYS A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 723
      removed outlier: 4.237A  pdb=" N   SER A 714 " --> pdb=" O   THR A 710 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   GLU A 715 " --> pdb=" O   GLN A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 729 through 743
    Processing helix  chain 'A' and resid 750 through 764
      removed outlier: 4.267A  pdb=" N   CYS A 764 " --> pdb=" O   ARG A 760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 786
      removed outlier: 3.582A  pdb=" N   ILE A 772 " --> pdb=" O   PRO A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 812
      removed outlier: 3.622A  pdb=" N   TYR A 804 " --> pdb=" O   TYR A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 827
      removed outlier: 3.857A  pdb=" N   LEU A 825 " --> pdb=" O   SER A 821 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   CYS A 826 " --> pdb=" O   GLU A 822 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LEU A 827 " --> pdb=" O   ILE A 823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 831 through 841
      removed outlier: 3.523A  pdb=" N   ILE A 835 " --> pdb=" O   LYS A 831 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 846 through 857
    Processing helix  chain 'A' and resid 861 through 871
    Processing helix  chain 'A' and resid 878 through 900
    Processing helix  chain 'A' and resid 908 through 922
      removed outlier: 3.638A  pdb=" N   TYR A 912 " --> pdb=" O   SER A 908 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 927 through 933
      removed outlier: 3.641A  pdb=" N   MET A 930 " --> pdb=" O   ASN A 927 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLU A 931 " --> pdb=" O   SER A 928 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   PHE A 933 " --> pdb=" O   MET A 930 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 937 through 945
    Processing helix  chain 'A' and resid 955 through 961
    Processing helix  chain 'A' and resid 963 through 973
    Processing helix  chain 'A' and resid 973 through 991
      removed outlier: 4.399A  pdb=" N   HIS A 979 " --> pdb=" O   HIS A 975 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 993 through 1003
    Processing helix  chain 'B' and resid 305 through 317
    Processing helix  chain 'B' and resid 318 through 321
      removed outlier: 3.608A  pdb=" N   ALA B 321 " --> pdb=" O   PRO B 318 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 318 through 321'
    Processing helix  chain 'B' and resid 327 through 333
    Processing helix  chain 'B' and resid 355 through 366
    Processing helix  chain 'B' and resid 366 through 372
      removed outlier: 3.525A  pdb=" N   ARG B 370 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LYS B 372 " --> pdb=" O   ASP B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 374 through 392
    Processing helix  chain 'B' and resid 411 through 416
    Processing helix  chain 'B' and resid 417 through 427
    Processing helix  chain 'B' and resid 431 through 445
    Processing helix  chain 'B' and resid 447 through 466
      removed outlier: 4.389A  pdb=" N   ASP B 464 " --> pdb=" O   LEU B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 500
      removed outlier: 4.962A  pdb=" N   LEU B 497 " --> pdb=" O   ASN B 493 " (cutoff:3.500A)
      removed outlier: 4.828A  pdb=" N   LEU B 498 " --> pdb=" O   GLY B 494 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 519
      removed outlier: 4.176A  pdb=" N   MET B 519 " --> pdb=" O   ILE B 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 527
      removed outlier: 3.568A  pdb=" N   ASP B 526 " --> pdb=" O   ASN B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 532 through 539
    Processing helix  chain 'B' and resid 542 through 547
      removed outlier: 3.889A  pdb=" N   SER B 546 " --> pdb=" O   LEU B 542 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ASP B 547 " --> pdb=" O   GLU B 543 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 542 through 547'
    Processing helix  chain 'B' and resid 552 through 572
    Processing helix  chain 'B' and resid 579 through 598
    Processing helix  chain 'B' and resid 600 through 604
      removed outlier: 3.529A  pdb=" N   VAL B 603 " --> pdb=" O   LEU B 600 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 605 through 628
      removed outlier: 3.800A  pdb=" N   THR B 628 " --> pdb=" O   GLU B 624 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 634 through 639
      removed outlier: 4.023A  pdb=" N   PHE B 639 " --> pdb=" O   GLY B 635 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 659
    Processing helix  chain 'B' and resid 660 through 671
    Processing helix  chain 'B' and resid 672 through 676
    Processing helix  chain 'B' and resid 680 through 701
      removed outlier: 3.658A  pdb=" N   ALA B 701 " --> pdb=" O   LYS B 697 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 723
      removed outlier: 4.426A  pdb=" N   SER B 714 " --> pdb=" O   THR B 710 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   GLU B 715 " --> pdb=" O   GLN B 711 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 724 through 726
      No H-bonds generated for 'chain 'B' and resid 724 through 726'
    Processing helix  chain 'B' and resid 729 through 743
    Processing helix  chain 'B' and resid 750 through 762
    Processing helix  chain 'B' and resid 768 through 786
      removed outlier: 3.561A  pdb=" N   ILE B 772 " --> pdb=" O   PRO B 768 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 800 through 812
      removed outlier: 3.627A  pdb=" N   TYR B 804 " --> pdb=" O   TYR B 800 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 817 through 826
      removed outlier: 3.605A  pdb=" N   CYS B 826 " --> pdb=" O   GLU B 822 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 831 through 841
      removed outlier: 4.072A  pdb=" N   LYS B 840 " --> pdb=" O   ASP B 836 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   LEU B 841 " --> pdb=" O   PHE B 837 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 846 through 857
    Processing helix  chain 'B' and resid 861 through 871
    Processing helix  chain 'B' and resid 878 through 903
      removed outlier: 4.699A  pdb=" N   GLU B 901 " --> pdb=" O   ILE B 897 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   LYS B 902 " --> pdb=" O   VAL B 898 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 909 through 922
    Processing helix  chain 'B' and resid 927 through 934
      removed outlier: 3.519A  pdb=" N   GLU B 931 " --> pdb=" O   SER B 928 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 939 through 945
      removed outlier: 4.035A  pdb=" N   PHE B 943 " --> pdb=" O   GLN B 939 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 950 through 954
    Processing helix  chain 'B' and resid 955 through 960
    Processing helix  chain 'B' and resid 963 through 972
    Processing helix  chain 'B' and resid 976 through 991
      removed outlier: 3.598A  pdb=" N   VAL B 980 " --> pdb=" O   MET B 976 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 993 through 1003
      removed outlier: 3.697A  pdb=" N   LEU B 997 " --> pdb=" O   ASP B 993 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 69 through 76
      removed outlier: 3.723A  pdb=" N   THR E  76 " --> pdb=" O   TRP E  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 69 through 76
      removed outlier: 3.737A  pdb=" N   THR F  76 " --> pdb=" O   TRP F  72 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 338 through 340
    Processing sheet with id=AA2, first strand: chain 'A' and resid 574 through 575
      removed outlier: 6.766A  pdb=" N   PHE F  13 " --> pdb=" O   VAL F  22 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   THR F  24 " --> pdb=" O   VAL F  11 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   VAL F  11 " --> pdb=" O   THR F  24 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   TYR F 171 " --> pdb=" O   ASN F 197 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ASN F 197 " --> pdb=" O   TYR F 171 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ILE F 193 " --> pdb=" O   TYR F 175 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575
      removed outlier: 8.409A  pdb=" N   VAL F  22 " --> pdb=" O   PHE F  68 " (cutoff:3.500A)
      removed outlier: 5.035A  pdb=" N   PHE F  68 " --> pdb=" O   VAL F  22 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   THR F  24 " --> pdb=" O   ALA F  66 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   ALA F  66 " --> pdb=" O   THR F  24 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   THR F  62 " --> pdb=" O   GLN F  28 " (cutoff:3.500A)
      removed outlier: 4.927A  pdb=" N   ALA F  30 " --> pdb=" O   ASN F  60 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   ASN F  60 " --> pdb=" O   ALA F  30 " (cutoff:3.500A)
      removed outlier: 5.300A  pdb=" N   PHE F  32 " --> pdb=" O   GLU F  58 " (cutoff:3.500A)
      removed outlier: 7.310A  pdb=" N   GLU F  58 " --> pdb=" O   PHE F  32 " (cutoff:3.500A)
      removed outlier: 5.542A  pdb=" N   GLN F  34 " --> pdb=" O   GLU F  56 " (cutoff:3.500A)
      removed outlier: 7.990A  pdb=" N   GLU F  56 " --> pdb=" O   GLN F  34 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   ILE F  59 " --> pdb=" O   ALA F 222 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LEU F  61 " --> pdb=" O   PHE F 220 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 339 through 340
    Processing sheet with id=AA5, first strand: chain 'B' and resid 574 through 575
      removed outlier: 4.470A  pdb=" N   GLU E  26 " --> pdb=" O   ASN E  65 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   ASN E  65 " --> pdb=" O   GLU E  26 " (cutoff:3.500A)
      removed outlier: 5.536A  pdb=" N   GLN E  28 " --> pdb=" O   VAL E  63 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   VAL E  63 " --> pdb=" O   GLN E  28 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ALA E  30 " --> pdb=" O   LEU E  61 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   LEU E  61 " --> pdb=" O   ALA E  30 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   PHE E  32 " --> pdb=" O   ILE E  59 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   ILE E  59 " --> pdb=" O   PHE E  32 " (cutoff:3.500A)
      removed outlier: 7.315A  pdb=" N   GLN E  34 " --> pdb=" O   LYS E  57 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   LYS E  57 " --> pdb=" O   GLN E  34 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LEU E  61 " --> pdb=" O   PHE E 220 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 574 through 575
      removed outlier: 6.698A  pdb=" N   PHE E  13 " --> pdb=" O   VAL E  22 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   THR E  24 " --> pdb=" O   VAL E  11 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   VAL E  11 " --> pdb=" O   THR E  24 " (cutoff:3.500A)
      removed outlier: 7.096A  pdb=" N   TYR E 171 " --> pdb=" O   ASN E 197 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ASN E 197 " --> pdb=" O   TYR E 171 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLN E 194 " --> pdb=" O   VAL E 233 " (cutoff:3.500A)

    763 hydrogen bonds defined for protein.
    2172 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: 5.09

  Time building geometry restraints manager: 4.05 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 2391
        1.31 -     1.44: 3992
        1.44 -     1.56: 7907
        1.56 -     1.69: 0
        1.69 -     1.81: 92
  Bond restraints: 14382
  Sorted by residual:
  bond pdb=" C   ASN A 598 "
       pdb=" O   ASN A 598 "
    ideal  model  delta    sigma   weight residual
    1.236  1.184  0.052 1.32e-02 5.74e+03 1.53e+01
  bond pdb=" C   ASN A 910 "
       pdb=" O   ASN A 910 "
    ideal  model  delta    sigma   weight residual
    1.236  1.189  0.047 1.26e-02 6.30e+03 1.41e+01
  bond pdb=" C   ASP A 911 "
       pdb=" O   ASP A 911 "
    ideal  model  delta    sigma   weight residual
    1.236  1.198  0.038 1.15e-02 7.56e+03 1.11e+01
  bond pdb=" C   ARG A 447 "
       pdb=" O   ARG A 447 "
    ideal  model  delta    sigma   weight residual
    1.235  1.196  0.039 1.26e-02 6.30e+03 9.69e+00
  bond pdb=" CA  ASP A 788 "
       pdb=" C   ASP A 788 "
    ideal  model  delta    sigma   weight residual
    1.523  1.486  0.037 1.32e-02 5.74e+03 8.07e+00
  ... (remaining 14377 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 18994
        2.51 -     5.02: 313
        5.02 -     7.53: 32
        7.53 -    10.04: 8
       10.04 -    12.55: 3
  Bond angle restraints: 19350
  Sorted by residual:
  angle pdb=" N   LYS B 660 "
        pdb=" CA  LYS B 660 "
        pdb=" C   LYS B 660 "
      ideal   model   delta    sigma   weight residual
     110.46   97.91   12.55 1.48e+00 4.57e-01 7.19e+01
  angle pdb=" N   PHE B 744 "
        pdb=" CA  PHE B 744 "
        pdb=" C   PHE B 744 "
      ideal   model   delta    sigma   weight residual
     109.83  100.76    9.07 1.27e+00 6.20e-01 5.10e+01
  angle pdb=" N   ARG A 447 "
        pdb=" CA  ARG A 447 "
        pdb=" C   ARG A 447 "
      ideal   model   delta    sigma   weight residual
     110.80   99.05   11.75 2.13e+00 2.20e-01 3.04e+01
  angle pdb=" C   ASN F 210 "
        pdb=" CA  ASN F 210 "
        pdb=" CB  ASN F 210 "
      ideal   model   delta    sigma   weight residual
     110.08  101.63    8.45 1.57e+00 4.06e-01 2.90e+01
  angle pdb=" N   ASN A 702 "
        pdb=" CA  ASN A 702 "
        pdb=" C   ASN A 702 "
      ideal   model   delta    sigma   weight residual
     111.28  105.89    5.39 1.09e+00 8.42e-01 2.45e+01
  ... (remaining 19345 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 7329
       17.98 -    35.96: 947
       35.96 -    53.95: 253
       53.95 -    71.93: 46
       71.93 -    89.91: 21
  Dihedral angle restraints: 8596
    sinusoidal: 3574
      harmonic: 5022
  Sorted by residual:
  dihedral pdb=" C   ASN F 210 "
           pdb=" N   ASN F 210 "
           pdb=" CA  ASN F 210 "
           pdb=" CB  ASN F 210 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.10  -10.50     0      2.50e+00 1.60e-01 1.76e+01
  dihedral pdb=" CA  GLU F 230 "
           pdb=" C   GLU F 230 "
           pdb=" N   MET F 231 "
           pdb=" CA  MET F 231 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.79  -18.21     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  THR E   8 "
           pdb=" C   THR E   8 "
           pdb=" N   ALA E   9 "
           pdb=" CA  ALA E   9 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.09  -17.91     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 8593 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1618
       0.046 -    0.093: 333
       0.093 -    0.139: 84
       0.139 -    0.186: 13
       0.186 -    0.232: 4
  Chirality restraints: 2052
  Sorted by residual:
  chirality pdb=" CA  TYR B1003 "
            pdb=" N   TYR B1003 "
            pdb=" C   TYR B1003 "
            pdb=" CB  TYR B1003 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CA  PHE A 907 "
            pdb=" N   PHE A 907 "
            pdb=" C   PHE A 907 "
            pdb=" CB  PHE A 907 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  ASN A 963 "
            pdb=" N   ASN A 963 "
            pdb=" C   ASN A 963 "
            pdb=" CB  ASN A 963 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.62e-01
  ... (remaining 2049 not shown)

  Planarity restraints: 2480
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B1003 "   -0.018 2.00e-02 2.50e+03   3.56e-02 1.27e+01
        pdb=" C   TYR B1003 "    0.062 2.00e-02 2.50e+03
        pdb=" O   TYR B1003 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   PHE B1004 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE E 195 "   -0.056 5.00e-02 4.00e+02   8.50e-02 1.16e+01
        pdb=" N   PRO E 196 "    0.147 5.00e-02 4.00e+02
        pdb=" CA  PRO E 196 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO E 196 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 409 "   -0.013 2.00e-02 2.50e+03   2.61e-02 6.83e+00
        pdb=" C   ILE B 409 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ILE B 409 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASN B 410 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 2477 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1099
        2.74 -     3.28: 15609
        3.28 -     3.82: 24104
        3.82 -     4.36: 28760
        4.36 -     4.90: 48426
  Nonbonded interactions: 117998
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 551 "
            pdb=" OG1 THR A 555 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   LYS B 785 "
            pdb=" NZ  LYS B 785 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" OE2 GLU E 174 "
            pdb=" NH2 ARG E 176 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" O   PHE A 559 "
            pdb=" OG1 THR A 562 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   SER A 573 "
            pdb=" NH2 ARG A 629 "
     model   vdw
     2.237 3.120
  ... (remaining 117993 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'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.560
  Check model and map are aligned:         0.140
  Set scattering table:                    0.130
  Process input model:                     33.420
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5810
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      :  0.005   0.055  14382  Z= 0.289
  Angle     :  0.806  12.553  19350  Z= 0.476
  Chirality :  0.043   0.232   2052
  Planarity :  0.005   0.085   2480
  Dihedral  : 17.600  89.912   5364
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.76 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 19.66 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.06 %
  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: -0.75 (0.20), residues: 1682
  helix:  0.48 (0.16), residues: 963
  sheet: -1.83 (0.44), residues: 112
  loop : -1.76 (0.24), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 958 
 HIS   0.004   0.001   HIS A 786 
 PHE   0.041   0.002   PHE F  32 
 TYR   0.038   0.002   TYR B1003 
 ARG   0.005   0.001   ARG A 447 

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 218
  time to evaluate  : 1.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  616 MET cc_start: 0.8397 (mmm) cc_final: 0.7900 (mmt)
REVERT: A  950 ASP cc_start: 0.6581 (p0) cc_final: 0.6357 (p0)
REVERT: B  406 SER cc_start: 0.6640 (t) cc_final: 0.6268 (m)
REVERT: B  607 GLU cc_start: 0.6734 (mp0) cc_final: 0.6529 (mp0)
REVERT: B  693 GLU cc_start: 0.6235 (mp0) cc_final: 0.5352 (mm-30)
REVERT: F  219 LYS cc_start: 0.8026 (mtpp) cc_final: 0.7631 (mtpp)
  outliers start: 7
  outliers final: 2
  residues processed: 224
  average time/residue: 0.2731
  time to fit residues: 89.8050
Evaluate side-chains
  189 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 187
  time to evaluate  : 1.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  231 MET
Chi-restraints excluded: chain E residue  233 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    8.9990
   chunk 127 optimal weight:    8.9990
   chunk 70 optimal weight:    8.9990
   chunk 43 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 131 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 80 optimal weight:    0.8980
   chunk 98 optimal weight:    0.7980
   chunk 152 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 ASN
A 503 HIS
A 614 ASN
A 797 ASN
B 591 ASN
B 609 HIS
** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 852 HIS
B 895 ASN
B 961 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5845
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14382  Z= 0.208
  Angle     :  0.587  11.503  19350  Z= 0.312
  Chirality :  0.041   0.287   2052
  Planarity :  0.004   0.076   2480
  Dihedral  :  4.650  33.251   1862
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.38 %
    Favored  : 76.65 %
  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: -0.30 (0.20), residues: 1682
  helix:  0.84 (0.17), residues: 963
  sheet: -1.70 (0.46), residues: 102
  loop : -1.56 (0.24), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 958 
 HIS   0.007   0.001   HIS B 852 
 PHE   0.016   0.002   PHE A 708 
 TYR   0.016   0.002   TYR B 951 
 ARG   0.006   0.001   ARG A 870 

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 220
  time to evaluate  : 1.697 
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  306 ASP cc_start: 0.5276 (OUTLIER) cc_final: 0.4923 (t0)
REVERT: A  381 PHE cc_start: 0.7940 (t80) cc_final: 0.7639 (t80)
REVERT: A  616 MET cc_start: 0.8458 (mmm) cc_final: 0.8173 (mmm)
REVERT: A  626 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7833 (mm-30)
REVERT: A  663 ASP cc_start: 0.6006 (m-30) cc_final: 0.5661 (m-30)
REVERT: B  331 LYS cc_start: 0.7543 (ptpt) cc_final: 0.7275 (pttp)
REVERT: B  406 SER cc_start: 0.6674 (t) cc_final: 0.6423 (m)
REVERT: B  544 PHE cc_start: 0.6679 (t80) cc_final: 0.6379 (t80)
REVERT: B  552 TYR cc_start: 0.5904 (OUTLIER) cc_final: 0.5356 (t80)
REVERT: B  578 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7777 (ttp)
REVERT: B  857 LYS cc_start: 0.5191 (tttt) cc_final: 0.4350 (ttmt)
  outliers start: 46
  outliers final: 21
  residues processed: 248
  average time/residue: 0.2812
  time to fit residues: 101.4453
Evaluate side-chains
  218 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 193
  time to evaluate  : 1.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  503 HIS
Chi-restraints excluded: chain A residue  544 PHE
Chi-restraints excluded: chain A residue  626 GLU
Chi-restraints excluded: chain A residue  668 GLU
Chi-restraints excluded: chain A residue  807 LEU
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain B residue  367 CYS
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  552 TYR
Chi-restraints excluded: chain B residue  578 MET
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  656 SER
Chi-restraints excluded: chain B residue  660 LYS
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  891 THR
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue  193 ILE
Chi-restraints excluded: chain F residue   67 PHE
Chi-restraints excluded: chain F residue  198 VAL
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  221 GLU
Chi-restraints excluded: chain F residue  235 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 126 optimal weight:    4.9990
   chunk 103 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 152 optimal weight:    0.7980
   chunk 165 optimal weight:    7.9990
   chunk 136 optimal weight:    0.0980
   chunk 151 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 122 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 332 HIS
A 503 HIS
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 698 GLN
B 852 HIS
B 961 ASN
E 210 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5851
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  14382  Z= 0.186
  Angle     :  0.554  10.704  19350  Z= 0.295
  Chirality :  0.040   0.229   2052
  Planarity :  0.004   0.074   2480
  Dihedral  :  4.358  29.548   1858
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 20.96 %
    Favored  : 75.94 %
  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: -0.31 (0.20), residues: 1682
  helix:  0.83 (0.16), residues: 972
  sheet: -1.50 (0.46), residues: 102
  loop : -1.64 (0.24), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 958 
 HIS   0.007   0.001   HIS B 852 
 PHE   0.024   0.001   PHE A 387 
 TYR   0.020   0.001   TYR A 625 
 ARG   0.004   0.000   ARG A 566 

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 214
  time to evaluate  : 1.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  306 ASP cc_start: 0.5343 (OUTLIER) cc_final: 0.4974 (t0)
REVERT: A  364 LYS cc_start: 0.7562 (tttt) cc_final: 0.6596 (ttmt)
REVERT: A  503 HIS cc_start: 0.7515 (OUTLIER) cc_final: 0.7164 (p-80)
REVERT: A  616 MET cc_start: 0.8405 (mmm) cc_final: 0.8159 (mmm)
REVERT: A  626 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7745 (mm-30)
REVERT: A  802 ARG cc_start: 0.6161 (ptt180) cc_final: 0.5153 (ptp90)
REVERT: A 1001 MET cc_start: 0.5614 (mmm) cc_final: 0.5269 (mmm)
REVERT: B  331 LYS cc_start: 0.7529 (ptpt) cc_final: 0.7289 (pttp)
REVERT: B  396 MET cc_start: 0.6203 (mmm) cc_final: 0.5979 (tpp)
REVERT: B  544 PHE cc_start: 0.6029 (t80) cc_final: 0.5562 (t80)
REVERT: B  552 TYR cc_start: 0.5714 (OUTLIER) cc_final: 0.4717 (t80)
REVERT: B  578 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7932 (ttp)
REVERT: B  763 LYS cc_start: 0.6482 (mptt) cc_final: 0.6216 (mptt)
REVERT: B  765 ASN cc_start: 0.4732 (OUTLIER) cc_final: 0.1419 (t0)
REVERT: E  206 MET cc_start: 0.5441 (mmm) cc_final: 0.4893 (mtp)
REVERT: F  176 ARG cc_start: 0.4813 (tmm160) cc_final: 0.4584 (ttp80)
  outliers start: 48
  outliers final: 26
  residues processed: 244
  average time/residue: 0.2785
  time to fit residues: 100.2641
Evaluate side-chains
  231 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 199
  time to evaluate  : 1.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  503 HIS
Chi-restraints excluded: chain A residue  544 PHE
Chi-restraints excluded: chain A residue  626 GLU
Chi-restraints excluded: chain A residue  668 GLU
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  531 MET
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  552 TYR
Chi-restraints excluded: chain B residue  578 MET
Chi-restraints excluded: chain B residue  656 SER
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  825 LEU
Chi-restraints excluded: chain B residue  891 THR
Chi-restraints excluded: chain E residue  173 VAL
Chi-restraints excluded: chain E residue  193 ILE
Chi-restraints excluded: chain E residue  194 GLN
Chi-restraints excluded: chain E residue  228 THR
Chi-restraints excluded: chain F residue   67 PHE
Chi-restraints excluded: chain F residue   76 THR
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  198 VAL
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  221 GLU
Chi-restraints excluded: chain F residue  226 THR
Chi-restraints excluded: chain F residue  235 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 151 optimal weight:    9.9990
   chunk 114 optimal weight:    3.9990
   chunk 79 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   chunk 102 optimal weight:    2.9990
   chunk 153 optimal weight:    8.9990
   chunk 162 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9990
   chunk 145 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 491 GLN
A 503 HIS
B 483 GLN
B 852 HIS
** F  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5970
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14382  Z= 0.259
  Angle     :  0.608  13.454  19350  Z= 0.323
  Chirality :  0.042   0.267   2052
  Planarity :  0.004   0.081   2480
  Dihedral  :  4.524  27.330   1858
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 20.76 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.35 (0.20), residues: 1682
  helix:  0.71 (0.16), residues: 958
  sheet: -1.51 (0.46), residues: 102
  loop : -1.45 (0.24), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP E  72 
 HIS   0.009   0.001   HIS B 852 
 PHE   0.027   0.002   PHE A 646 
 TYR   0.040   0.002   TYR A 625 
 ARG   0.005   0.000   ARG A 480 

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 220
  time to evaluate  : 1.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  306 ASP cc_start: 0.5198 (OUTLIER) cc_final: 0.4895 (t0)
REVERT: A  364 LYS cc_start: 0.7608 (tttt) cc_final: 0.6562 (ttmt)
REVERT: A  368 ASP cc_start: 0.7978 (p0) cc_final: 0.7775 (p0)
REVERT: A  389 GLU cc_start: 0.7043 (pp20) cc_final: 0.6795 (pp20)
REVERT: A  442 LEU cc_start: 0.6956 (mt) cc_final: 0.6737 (mt)
REVERT: A  480 ARG cc_start: 0.7156 (mpt180) cc_final: 0.6857 (mmt90)
REVERT: A  503 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.6822 (p-80)
REVERT: A  616 MET cc_start: 0.8409 (mmm) cc_final: 0.8154 (mmm)
REVERT: A  626 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7834 (mm-30)
REVERT: A  647 MET cc_start: 0.7045 (tpt) cc_final: 0.5355 (tpt)
REVERT: A  687 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.5692 (t80)
REVERT: A  958 TRP cc_start: 0.6887 (OUTLIER) cc_final: 0.6093 (m-10)
REVERT: A 1001 MET cc_start: 0.5708 (mmm) cc_final: 0.5437 (mmm)
REVERT: B  331 LYS cc_start: 0.7569 (ptpt) cc_final: 0.7353 (pttp)
REVERT: B  396 MET cc_start: 0.6489 (mmm) cc_final: 0.6272 (tpp)
REVERT: B  552 TYR cc_start: 0.5971 (OUTLIER) cc_final: 0.4948 (t80)
REVERT: B  578 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7938 (ttp)
REVERT: B  765 ASN cc_start: 0.4890 (OUTLIER) cc_final: 0.1529 (t0)
REVERT: B  976 MET cc_start: 0.5798 (tmm) cc_final: 0.4563 (tmm)
  outliers start: 72
  outliers final: 43
  residues processed: 267
  average time/residue: 0.2631
  time to fit residues: 104.7297
Evaluate side-chains
  256 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 205
  time to evaluate  : 1.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  503 HIS
Chi-restraints excluded: chain A residue  544 PHE
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain A residue  626 GLU
Chi-restraints excluded: chain A residue  668 GLU
Chi-restraints excluded: chain A residue  671 CYS
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  712 PHE
Chi-restraints excluded: chain A residue  748 ASP
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain A residue  874 ILE
Chi-restraints excluded: chain A residue  957 SER
Chi-restraints excluded: chain A residue  958 TRP
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  451 SER
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  531 MET
Chi-restraints excluded: chain B residue  552 TYR
Chi-restraints excluded: chain B residue  578 MET
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  656 SER
Chi-restraints excluded: chain B residue  660 LYS
Chi-restraints excluded: chain B residue  689 VAL
Chi-restraints excluded: chain B residue  704 MET
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  825 LEU
Chi-restraints excluded: chain B residue  853 LEU
Chi-restraints excluded: chain B residue  891 THR
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   29 THR
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue  173 VAL
Chi-restraints excluded: chain E residue  193 ILE
Chi-restraints excluded: chain E residue  194 GLN
Chi-restraints excluded: chain F residue   67 PHE
Chi-restraints excluded: chain F residue   76 THR
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  198 VAL
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  221 GLU
Chi-restraints excluded: chain F residue  226 THR
Chi-restraints excluded: chain F residue  235 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 135 optimal weight:    0.9980
   chunk 92 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 120 optimal weight:    4.9990
   chunk 67 optimal weight:    6.9990
   chunk 138 optimal weight:   10.0000
   chunk 112 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   chunk 82 optimal weight:    0.5980
   chunk 145 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN
A 895 ASN
B 428 GLN
B 563 ASN
B 852 HIS
B 979 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5908
moved from start:          0.2861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  14382  Z= 0.188
  Angle     :  0.561  10.492  19350  Z= 0.298
  Chirality :  0.040   0.201   2052
  Planarity :  0.004   0.076   2480
  Dihedral  :  4.428  27.281   1858
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 21.67 %
    Favored  : 74.19 %
  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: -0.18 (0.20), residues: 1682
  helix:  0.87 (0.17), residues: 946
  sheet: -1.33 (0.47), residues: 102
  loop : -1.39 (0.24), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F  72 
 HIS   0.009   0.001   HIS B 852 
 PHE   0.030   0.001   PHE B 712 
 TYR   0.045   0.002   TYR A 625 
 ARG   0.003   0.000   ARG A 629 

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 214
  time to evaluate  : 1.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  306 ASP cc_start: 0.5264 (OUTLIER) cc_final: 0.4955 (t0)
REVERT: A  364 LYS cc_start: 0.7545 (tttt) cc_final: 0.6688 (ttmt)
REVERT: A  381 PHE cc_start: 0.7784 (t80) cc_final: 0.7500 (t80)
REVERT: A  389 GLU cc_start: 0.7042 (pp20) cc_final: 0.6765 (pp20)
REVERT: A  503 HIS cc_start: 0.7521 (OUTLIER) cc_final: 0.6955 (p90)
REVERT: A  616 MET cc_start: 0.8428 (mmm) cc_final: 0.8188 (mmm)
REVERT: A  626 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7798 (mm-30)
REVERT: A  647 MET cc_start: 0.7032 (tpt) cc_final: 0.5408 (tpt)
REVERT: A  687 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.5638 (t80)
REVERT: A  941 ASP cc_start: 0.4837 (m-30) cc_final: 0.4532 (m-30)
REVERT: A 1001 MET cc_start: 0.5705 (mmm) cc_final: 0.5440 (mmm)
REVERT: B  331 LYS cc_start: 0.7565 (ptpt) cc_final: 0.7351 (pttp)
REVERT: B  552 TYR cc_start: 0.6072 (OUTLIER) cc_final: 0.5105 (t80)
REVERT: B  578 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7928 (ttp)
REVERT: B  624 GLU cc_start: 0.5748 (tp30) cc_final: 0.5535 (tp30)
REVERT: B  711 GLN cc_start: 0.6657 (tm-30) cc_final: 0.6103 (tt0)
REVERT: B  763 LYS cc_start: 0.6698 (mptt) cc_final: 0.6362 (mptt)
REVERT: B  765 ASN cc_start: 0.4841 (OUTLIER) cc_final: 0.1617 (t0)
REVERT: B  976 MET cc_start: 0.5681 (tmm) cc_final: 0.4714 (tmm)
REVERT: B  986 GLU cc_start: 0.7119 (pp20) cc_final: 0.6805 (pp20)
  outliers start: 64
  outliers final: 39
  residues processed: 258
  average time/residue: 0.2687
  time to fit residues: 103.4041
Evaluate side-chains
  250 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 204
  time to evaluate  : 1.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  503 HIS
Chi-restraints excluded: chain A residue  544 PHE
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain A residue  626 GLU
Chi-restraints excluded: chain A residue  668 GLU
Chi-restraints excluded: chain A residue  671 CYS
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  712 PHE
Chi-restraints excluded: chain A residue  748 ASP
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain B residue  451 SER
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  531 MET
Chi-restraints excluded: chain B residue  552 TYR
Chi-restraints excluded: chain B residue  578 MET
Chi-restraints excluded: chain B residue  602 SER
Chi-restraints excluded: chain B residue  656 SER
Chi-restraints excluded: chain B residue  660 LYS
Chi-restraints excluded: chain B residue  676 ILE
Chi-restraints excluded: chain B residue  689 VAL
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  825 LEU
Chi-restraints excluded: chain B residue  891 THR
Chi-restraints excluded: chain E residue   52 ILE
Chi-restraints excluded: chain E residue  173 VAL
Chi-restraints excluded: chain E residue  193 ILE
Chi-restraints excluded: chain E residue  194 GLN
Chi-restraints excluded: chain E residue  228 THR
Chi-restraints excluded: chain F residue   67 PHE
Chi-restraints excluded: chain F residue   76 THR
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  191 ILE
Chi-restraints excluded: chain F residue  198 VAL
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  221 GLU
Chi-restraints excluded: chain F residue  226 THR
Chi-restraints excluded: chain F residue  235 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 54 optimal weight:    0.2980
   chunk 146 optimal weight:    7.9990
   chunk 32 optimal weight:    0.6980
   chunk 95 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 162 optimal weight:    8.9990
   chunk 134 optimal weight:    0.6980
   chunk 75 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 503 HIS
B 979 HIS
** F  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5901
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14382  Z= 0.186
  Angle     :  0.555   9.423  19350  Z= 0.297
  Chirality :  0.040   0.217   2052
  Planarity :  0.004   0.074   2480
  Dihedral  :  4.415  26.988   1858
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 22.06 %
    Favored  : 73.87 %
  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: -0.24 (0.20), residues: 1682
  helix:  0.82 (0.17), residues: 963
  sheet: -1.25 (0.47), residues: 102
  loop : -1.49 (0.24), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F  72 
 HIS   0.011   0.001   HIS B 852 
 PHE   0.037   0.002   PHE B 712 
 TYR   0.044   0.002   TYR A 625 
 ARG   0.002   0.000   ARG A 480 

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 229
  time to evaluate  : 1.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  306 ASP cc_start: 0.5270 (OUTLIER) cc_final: 0.4894 (t0)
REVERT: A  364 LYS cc_start: 0.7555 (tttt) cc_final: 0.6697 (ttmt)
REVERT: A  381 PHE cc_start: 0.7780 (t80) cc_final: 0.7457 (t80)
REVERT: A  389 GLU cc_start: 0.7011 (pp20) cc_final: 0.6763 (pp20)
REVERT: A  616 MET cc_start: 0.8439 (mmm) cc_final: 0.8190 (mmm)
REVERT: A  647 MET cc_start: 0.7088 (tpt) cc_final: 0.5472 (tpt)
REVERT: A  687 TYR cc_start: 0.7119 (OUTLIER) cc_final: 0.5604 (t80)
REVERT: A  941 ASP cc_start: 0.4768 (m-30) cc_final: 0.4452 (m-30)
REVERT: A 1001 MET cc_start: 0.5695 (mmm) cc_final: 0.5459 (mmm)
REVERT: B  331 LYS cc_start: 0.7701 (ptpt) cc_final: 0.7471 (pttp)
REVERT: B  552 TYR cc_start: 0.5830 (OUTLIER) cc_final: 0.5024 (t80)
REVERT: B  578 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7848 (ttp)
REVERT: B  711 GLN cc_start: 0.6721 (tm-30) cc_final: 0.6169 (tt0)
REVERT: B  763 LYS cc_start: 0.6645 (mptt) cc_final: 0.6241 (mptt)
REVERT: B  765 ASN cc_start: 0.4868 (OUTLIER) cc_final: 0.1853 (t0)
REVERT: B  976 MET cc_start: 0.5660 (tmm) cc_final: 0.4988 (tmm)
REVERT: B  986 GLU cc_start: 0.7167 (pp20) cc_final: 0.6809 (pp20)
  outliers start: 63
  outliers final: 44
  residues processed: 271
  average time/residue: 0.2629
  time to fit residues: 106.8085
Evaluate side-chains
  264 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 215
  time to evaluate  : 1.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  503 HIS
Chi-restraints excluded: chain A residue  544 PHE
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain A residue  668 GLU
Chi-restraints excluded: chain A residue  671 CYS
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  748 ASP
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  957 SER
Chi-restraints excluded: chain A residue  958 TRP
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  367 CYS
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  451 SER
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  552 TYR
Chi-restraints excluded: chain B residue  578 MET
Chi-restraints excluded: chain B residue  602 SER
Chi-restraints excluded: chain B residue  656 SER
Chi-restraints excluded: chain B residue  660 LYS
Chi-restraints excluded: chain B residue  676 ILE
Chi-restraints excluded: chain B residue  689 VAL
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  740 LEU
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  825 LEU
Chi-restraints excluded: chain B residue  891 THR
Chi-restraints excluded: chain E residue   29 THR
Chi-restraints excluded: chain E residue   31 SER
Chi-restraints excluded: chain E residue  173 VAL
Chi-restraints excluded: chain E residue  193 ILE
Chi-restraints excluded: chain E residue  194 GLN
Chi-restraints excluded: chain E residue  223 LEU
Chi-restraints excluded: chain F residue   67 PHE
Chi-restraints excluded: chain F residue   69 ASP
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  191 ILE
Chi-restraints excluded: chain F residue  198 VAL
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  221 GLU
Chi-restraints excluded: chain F residue  226 THR
Chi-restraints excluded: chain F residue  235 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 156 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 92 optimal weight:    5.9990
   chunk 118 optimal weight:    0.8980
   chunk 91 optimal weight:    0.8980
   chunk 136 optimal weight:    0.5980
   chunk 90 optimal weight:    0.9980
   chunk 161 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   chunk 98 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 895 ASN
B 852 HIS
B 979 HIS
** F  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5917
moved from start:          0.3366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14382  Z= 0.199
  Angle     :  0.571   9.153  19350  Z= 0.306
  Chirality :  0.041   0.234   2052
  Planarity :  0.004   0.074   2480
  Dihedral  :  4.402  26.963   1858
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 22.12 %
    Favored  : 73.22 %
  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: -0.25 (0.20), residues: 1682
  helix:  0.82 (0.17), residues: 957
  sheet: -1.60 (0.45), residues: 112
  loop : -1.41 (0.24), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F  72 
 HIS   0.010   0.001   HIS B 852 
 PHE   0.049   0.002   PHE B 708 
 TYR   0.043   0.002   TYR A 625 
 ARG   0.004   0.000   ARG A 502 

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 218
  time to evaluate  : 1.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  306 ASP cc_start: 0.5234 (OUTLIER) cc_final: 0.4961 (t0)
REVERT: A  364 LYS cc_start: 0.7590 (tttt) cc_final: 0.6734 (ttmt)
REVERT: A  381 PHE cc_start: 0.7841 (t80) cc_final: 0.7511 (t80)
REVERT: A  384 LEU cc_start: 0.7569 (tp) cc_final: 0.7307 (mm)
REVERT: A  389 GLU cc_start: 0.7063 (pp20) cc_final: 0.6817 (pp20)
REVERT: A  569 MET cc_start: 0.6343 (OUTLIER) cc_final: 0.4228 (mtt)
REVERT: A  616 MET cc_start: 0.8398 (mmm) cc_final: 0.8136 (mmm)
REVERT: A  647 MET cc_start: 0.7146 (tpt) cc_final: 0.5499 (tpt)
REVERT: A  687 TYR cc_start: 0.7117 (OUTLIER) cc_final: 0.5442 (t80)
REVERT: A  722 PHE cc_start: 0.6545 (t80) cc_final: 0.6288 (t80)
REVERT: A 1001 MET cc_start: 0.5667 (mmm) cc_final: 0.5453 (mmm)
REVERT: B  384 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6976 (mm)
REVERT: B  578 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7837 (ttp)
REVERT: B  585 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7152 (tp)
REVERT: B  711 GLN cc_start: 0.6753 (tm-30) cc_final: 0.6272 (tt0)
REVERT: B  713 ILE cc_start: 0.7062 (tp) cc_final: 0.6169 (tp)
REVERT: B  763 LYS cc_start: 0.6631 (mptt) cc_final: 0.6179 (mptt)
REVERT: B  765 ASN cc_start: 0.4839 (OUTLIER) cc_final: 0.1866 (t0)
REVERT: B  976 MET cc_start: 0.5795 (tmm) cc_final: 0.5098 (tmm)
REVERT: B  986 GLU cc_start: 0.7333 (pp20) cc_final: 0.7012 (pp20)
REVERT: E  236 GLU cc_start: 0.4373 (OUTLIER) cc_final: 0.3973 (mp0)
REVERT: F  176 ARG cc_start: 0.4580 (tmm160) cc_final: 0.4275 (tmm160)
REVERT: F  231 MET cc_start: 0.2239 (pmm) cc_final: 0.1743 (pmm)
  outliers start: 72
  outliers final: 51
  residues processed: 267
  average time/residue: 0.2611
  time to fit residues: 104.5750
Evaluate side-chains
  266 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 207
  time to evaluate  : 1.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  367 CYS
Chi-restraints excluded: chain A residue  544 PHE
Chi-restraints excluded: chain A residue  569 MET
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain A residue  668 GLU
Chi-restraints excluded: chain A residue  671 CYS
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  712 PHE
Chi-restraints excluded: chain A residue  748 ASP
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  957 SER
Chi-restraints excluded: chain A residue  958 TRP
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  367 CYS
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  451 SER
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  575 SER
Chi-restraints excluded: chain B residue  578 MET
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  602 SER
Chi-restraints excluded: chain B residue  656 SER
Chi-restraints excluded: chain B residue  660 LYS
Chi-restraints excluded: chain B residue  676 ILE
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  710 THR
Chi-restraints excluded: chain B residue  740 LEU
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  825 LEU
Chi-restraints excluded: chain B residue  891 THR
Chi-restraints excluded: chain E residue   29 THR
Chi-restraints excluded: chain E residue   31 SER
Chi-restraints excluded: chain E residue  173 VAL
Chi-restraints excluded: chain E residue  193 ILE
Chi-restraints excluded: chain E residue  194 GLN
Chi-restraints excluded: chain E residue  223 LEU
Chi-restraints excluded: chain E residue  228 THR
Chi-restraints excluded: chain E residue  236 GLU
Chi-restraints excluded: chain F residue   67 PHE
Chi-restraints excluded: chain F residue   69 ASP
Chi-restraints excluded: chain F residue   76 THR
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  191 ILE
Chi-restraints excluded: chain F residue  193 ILE
Chi-restraints excluded: chain F residue  198 VAL
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  221 GLU
Chi-restraints excluded: chain F residue  226 THR
Chi-restraints excluded: chain F residue  235 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 64 optimal weight:    0.4980
   chunk 96 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 102 optimal weight:    0.7980
   chunk 110 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 127 optimal weight:    3.9990
   chunk 147 optimal weight:   10.0000
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 852 HIS
B 979 HIS
** F  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5917
moved from start:          0.3589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14382  Z= 0.198
  Angle     :  0.598  14.804  19350  Z= 0.316
  Chirality :  0.042   0.382   2052
  Planarity :  0.004   0.073   2480
  Dihedral  :  4.426  26.792   1858
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 22.38 %
    Favored  : 73.09 %
  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: -0.27 (0.20), residues: 1682
  helix:  0.80 (0.17), residues: 954
  sheet: -1.68 (0.46), residues: 108
  loop : -1.39 (0.24), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F  72 
 HIS   0.011   0.001   HIS B 852 
 PHE   0.039   0.002   PHE B 708 
 TYR   0.047   0.002   TYR A 625 
 ARG   0.003   0.000   ARG B 627 

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 220
  time to evaluate  : 1.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  306 ASP cc_start: 0.5077 (OUTLIER) cc_final: 0.4854 (t0)
REVERT: A  364 LYS cc_start: 0.7632 (tttt) cc_final: 0.6788 (ttmt)
REVERT: A  381 PHE cc_start: 0.7774 (t80) cc_final: 0.7486 (t80)
REVERT: A  384 LEU cc_start: 0.7619 (tp) cc_final: 0.7359 (mm)
REVERT: A  389 GLU cc_start: 0.7124 (pp20) cc_final: 0.6905 (pp20)
REVERT: A  569 MET cc_start: 0.6432 (OUTLIER) cc_final: 0.5107 (mmt)
REVERT: A  616 MET cc_start: 0.8390 (mmm) cc_final: 0.8124 (mmm)
REVERT: A  647 MET cc_start: 0.7167 (tpt) cc_final: 0.5535 (tpt)
REVERT: A  687 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.5581 (t80)
REVERT: A  722 PHE cc_start: 0.6545 (t80) cc_final: 0.6272 (t80)
REVERT: B  578 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7850 (ttp)
REVERT: B  585 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7153 (tp)
REVERT: B  711 GLN cc_start: 0.6693 (tm-30) cc_final: 0.6187 (tt0)
REVERT: B  763 LYS cc_start: 0.6518 (mptt) cc_final: 0.6081 (mptt)
REVERT: B  765 ASN cc_start: 0.4836 (OUTLIER) cc_final: 0.1919 (t0)
REVERT: B  976 MET cc_start: 0.5625 (tmm) cc_final: 0.4816 (tmm)
REVERT: B  986 GLU cc_start: 0.7364 (pp20) cc_final: 0.7017 (pp20)
REVERT: F  176 ARG cc_start: 0.4513 (tmm160) cc_final: 0.4268 (tmm160)
REVERT: F  231 MET cc_start: 0.2235 (pmm) cc_final: 0.1730 (pmm)
  outliers start: 70
  outliers final: 48
  residues processed: 266
  average time/residue: 0.3004
  time to fit residues: 119.7495
Evaluate side-chains
  264 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 210
  time to evaluate  : 1.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  367 CYS
Chi-restraints excluded: chain A residue  544 PHE
Chi-restraints excluded: chain A residue  552 TYR
Chi-restraints excluded: chain A residue  569 MET
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain A residue  668 GLU
Chi-restraints excluded: chain A residue  671 CYS
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  712 PHE
Chi-restraints excluded: chain A residue  748 ASP
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  958 TRP
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  367 CYS
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  451 SER
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  575 SER
Chi-restraints excluded: chain B residue  578 MET
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  602 SER
Chi-restraints excluded: chain B residue  656 SER
Chi-restraints excluded: chain B residue  660 LYS
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  740 LEU
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  825 LEU
Chi-restraints excluded: chain B residue  891 THR
Chi-restraints excluded: chain E residue   29 THR
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue  173 VAL
Chi-restraints excluded: chain E residue  193 ILE
Chi-restraints excluded: chain E residue  194 GLN
Chi-restraints excluded: chain E residue  223 LEU
Chi-restraints excluded: chain E residue  228 THR
Chi-restraints excluded: chain F residue   67 PHE
Chi-restraints excluded: chain F residue   69 ASP
Chi-restraints excluded: chain F residue   76 THR
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  191 ILE
Chi-restraints excluded: chain F residue  193 ILE
Chi-restraints excluded: chain F residue  198 VAL
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  221 GLU
Chi-restraints excluded: chain F residue  226 THR
Chi-restraints excluded: chain F residue  235 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 155 optimal weight:    0.6980
   chunk 141 optimal weight:    0.0980
   chunk 150 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 118 optimal weight:    5.9990
   chunk 46 optimal weight:    0.5980
   chunk 136 optimal weight:    0.7980
   chunk 142 optimal weight:    1.9990
   chunk 99 optimal weight:    0.5980
   chunk 159 optimal weight:    0.0670
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 852 HIS
B 979 HIS
F  34 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5855
moved from start:          0.3759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14382  Z= 0.171
  Angle     :  0.594  12.899  19350  Z= 0.313
  Chirality :  0.041   0.274   2052
  Planarity :  0.004   0.072   2480
  Dihedral  :  4.377  27.272   1858
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 23.87 %
    Favored  : 72.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.17 (0.20), residues: 1682
  helix:  0.88 (0.17), residues: 946
  sheet: -1.45 (0.45), residues: 118
  loop : -1.35 (0.24), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 601 
 HIS   0.012   0.001   HIS B 852 
 PHE   0.035   0.001   PHE A 646 
 TYR   0.040   0.002   TYR B 552 
 ARG   0.004   0.000   ARG A 359 

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 223
  time to evaluate  : 1.728 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  364 LYS cc_start: 0.7548 (tttt) cc_final: 0.6639 (ttmt)
REVERT: A  381 PHE cc_start: 0.7767 (t80) cc_final: 0.7443 (t80)
REVERT: A  384 LEU cc_start: 0.7595 (tp) cc_final: 0.7327 (mm)
REVERT: A  569 MET cc_start: 0.6017 (mpp) cc_final: 0.5022 (mpp)
REVERT: A  616 MET cc_start: 0.8422 (mmm) cc_final: 0.8186 (mmm)
REVERT: A  647 MET cc_start: 0.7075 (tpt) cc_final: 0.5261 (tpt)
REVERT: A  687 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.5665 (t80)
REVERT: B  390 LYS cc_start: 0.6249 (ttpt) cc_final: 0.5861 (pttt)
REVERT: B  763 LYS cc_start: 0.6491 (mptt) cc_final: 0.6134 (mptt)
REVERT: B  976 MET cc_start: 0.5756 (tmm) cc_final: 0.4982 (tmm)
REVERT: B  986 GLU cc_start: 0.7339 (pp20) cc_final: 0.6992 (pp20)
  outliers start: 51
  outliers final: 40
  residues processed: 257
  average time/residue: 0.2712
  time to fit residues: 103.1176
Evaluate side-chains
  245 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 204
  time to evaluate  : 1.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  367 CYS
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain A residue  668 GLU
Chi-restraints excluded: chain A residue  671 CYS
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  748 ASP
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  957 SER
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  451 SER
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  656 SER
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  713 ILE
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  825 LEU
Chi-restraints excluded: chain B residue  891 THR
Chi-restraints excluded: chain E residue  173 VAL
Chi-restraints excluded: chain E residue  193 ILE
Chi-restraints excluded: chain E residue  194 GLN
Chi-restraints excluded: chain E residue  223 LEU
Chi-restraints excluded: chain F residue   67 PHE
Chi-restraints excluded: chain F residue   76 THR
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  191 ILE
Chi-restraints excluded: chain F residue  193 ILE
Chi-restraints excluded: chain F residue  198 VAL
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  221 GLU
Chi-restraints excluded: chain F residue  226 THR
Chi-restraints excluded: chain F residue  235 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 75 optimal weight:    0.7980
   chunk 110 optimal weight:    0.6980
   chunk 167 optimal weight:    5.9990
   chunk 154 optimal weight:    7.9990
   chunk 133 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 102 optimal weight:    0.0870
   chunk 81 optimal weight:    0.5980
   chunk 105 optimal weight:    1.9990
   chunk 141 optimal weight:    2.9990
   overall best weight:    0.8360

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

Flipped N/Q/H residues before XYZ refinement:
** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 895 ASN
B 852 HIS
B 979 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5913
moved from start:          0.3899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14382  Z= 0.211
  Angle     :  0.631  13.531  19350  Z= 0.331
  Chirality :  0.042   0.344   2052
  Planarity :  0.004   0.073   2480
  Dihedral  :  4.427  27.075   1858
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 24.39 %
    Favored  : 72.12 %
  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: -0.26 (0.20), residues: 1682
  helix:  0.80 (0.17), residues: 952
  sheet: -1.42 (0.45), residues: 118
  loop : -1.41 (0.24), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP F  72 
 HIS   0.012   0.001   HIS B 852 
 PHE   0.035   0.002   PHE B 708 
 TYR   0.048   0.002   TYR A 611 
 ARG   0.009   0.001   ARG F 176 

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 206
  time to evaluate  : 1.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  364 LYS cc_start: 0.7547 (tttt) cc_final: 0.6636 (ttmt)
REVERT: A  381 PHE cc_start: 0.7782 (t80) cc_final: 0.7454 (t80)
REVERT: A  384 LEU cc_start: 0.7578 (tp) cc_final: 0.7341 (mm)
REVERT: A  569 MET cc_start: 0.6004 (OUTLIER) cc_final: 0.4969 (mpp)
REVERT: A  616 MET cc_start: 0.8395 (mmm) cc_final: 0.8189 (mmm)
REVERT: A  647 MET cc_start: 0.7144 (tpt) cc_final: 0.5276 (tpt)
REVERT: A  687 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.5567 (t80)
REVERT: B  763 LYS cc_start: 0.6518 (mptt) cc_final: 0.6084 (mptt)
REVERT: B  765 ASN cc_start: 0.4799 (OUTLIER) cc_final: 0.1937 (t0)
REVERT: B  976 MET cc_start: 0.5858 (tmm) cc_final: 0.5168 (tmm)
REVERT: B  986 GLU cc_start: 0.7348 (pp20) cc_final: 0.7007 (pp20)
REVERT: E   75 MET cc_start: 0.3447 (ppp) cc_final: 0.2982 (ppp)
  outliers start: 54
  outliers final: 41
  residues processed: 242
  average time/residue: 0.2663
  time to fit residues: 96.9481
Evaluate side-chains
  244 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 200
  time to evaluate  : 1.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  367 CYS
Chi-restraints excluded: chain A residue  569 MET
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain A residue  668 GLU
Chi-restraints excluded: chain A residue  671 CYS
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  748 ASP
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  874 ILE
Chi-restraints excluded: chain A residue  930 MET
Chi-restraints excluded: chain A residue  957 SER
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  367 CYS
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  451 SER
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  656 SER
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  740 LEU
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  825 LEU
Chi-restraints excluded: chain B residue  891 THR
Chi-restraints excluded: chain E residue  173 VAL
Chi-restraints excluded: chain E residue  193 ILE
Chi-restraints excluded: chain E residue  194 GLN
Chi-restraints excluded: chain E residue  223 LEU
Chi-restraints excluded: chain F residue   67 PHE
Chi-restraints excluded: chain F residue   76 THR
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  191 ILE
Chi-restraints excluded: chain F residue  193 ILE
Chi-restraints excluded: chain F residue  198 VAL
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  221 GLU
Chi-restraints excluded: chain F residue  226 THR
Chi-restraints excluded: chain F residue  235 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 122 optimal weight:    0.0060
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 133 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 137 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 24 optimal weight:    0.8980
   chunk 117 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.7396

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

Flipped N/Q/H residues before XYZ refinement:
A 654 ASN
A 895 ASN
A 973 ASN
B 852 HIS
B 979 HIS
F  34 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4772 r_free = 0.4772 target = 0.247742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.214545 restraints weight = 17197.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.4475 rms_B_bonded: 2.18
r_work: 0.4338 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.4338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5968
moved from start:          0.4011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14382  Z= 0.200
  Angle     :  0.622  13.187  19350  Z= 0.327
  Chirality :  0.042   0.322   2052
  Planarity :  0.004   0.073   2480
  Dihedral  :  4.431  26.955   1858
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 24.51 %
    Favored  : 71.99 %
  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: -0.35 (0.20), residues: 1682
  helix:  0.75 (0.17), residues: 960
  sheet: -1.42 (0.44), residues: 112
  loop : -1.53 (0.24), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 601 
 HIS   0.012   0.001   HIS B 852 
 PHE   0.034   0.002   PHE B 708 
 TYR   0.055   0.002   TYR A 552 
 ARG   0.005   0.000   ARG A 480 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3075.67 seconds
wall clock time: 58 minutes 17.12 seconds (3497.12 seconds total)