Starting phenix.real_space_refine
on Sat Jun 14 15:37:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pcz_17596/06_2025/8pcz_17596.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pcz_17596/06_2025/8pcz_17596.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pcz_17596/06_2025/8pcz_17596.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pcz_17596/06_2025/8pcz_17596.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pcz_17596/06_2025/8pcz_17596.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pcz_17596/06_2025/8pcz_17596.cif"
  }
  resolution = 3.21
  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=   0.032
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      84      5.16       5
     C   10574      2.51       5
     N    2686      2.21       5
     O    2832      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16176
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8088
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1023, 8088
          Classifications: {'peptide': 1023}
          Link IDs: {'PTRANS': 30, 'TRANS': 992}
          Chain breaks: 5
  Restraints were copied for chains:
    B
  Time building chain proxies: 19.36, per 1000 atoms: 1.20
  Number of scatterers: 16176
  At special positions: 0
  Unit cell: (112.86, 152.988, 122.892, 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      84     16.00
     O    2832      8.00
     N    2686      7.00
     C   10574      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.07
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3860

  Finding SS restraints...
    Secondary structure from input PDB file:
      96 helices and 8 sheets defined
      78.2% alpha, 4.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 76 through 95
      removed outlier: 3.565A  pdb=" N   PHE A  80 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 120
      removed outlier: 3.986A  pdb=" N   VAL A 105 " --> pdb=" O   PRO A 101 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ASN A 119 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 4.644A  pdb=" N   ASP A 129 " --> pdb=" O   GLU A 125 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   VAL A 130 " --> pdb=" O   HIS A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 153
      Proline residue:  A 144  - end of helix
    Processing helix  chain 'A' and resid 155 through 162
    Processing helix  chain 'A' and resid 162 through 188
      removed outlier: 3.574A  pdb=" N   GLY A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 207
      removed outlier: 3.564A  pdb=" N   ALA A 207 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 221
      removed outlier: 3.924A  pdb=" N   LEU A 216 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 254
      removed outlier: 3.566A  pdb=" N   GLY A 227 " --> pdb=" O   SER A 223 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   THR A 228 " --> pdb=" O   LYS A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 273
    Processing helix  chain 'A' and resid 273 through 291
    Processing helix  chain 'A' and resid 296 through 317
    Processing helix  chain 'A' and resid 322 through 337
    Processing helix  chain 'A' and resid 338 through 341
    Processing helix  chain 'A' and resid 342 through 376
      removed outlier: 3.637A  pdb=" N   ARG A 351 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 380
    Processing helix  chain 'A' and resid 381 through 412
      removed outlier: 3.835A  pdb=" N   TRP A 385 " --> pdb=" O   ASP A 381 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE A 386 " --> pdb=" O   LYS A 382 " (cutoff:3.500A)
      Proline residue:  A 408  - end of helix
      removed outlier: 3.997A  pdb=" N   ARG A 412 " --> pdb=" O   PRO A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 428
    Processing helix  chain 'A' and resid 432 through 447
    Processing helix  chain 'A' and resid 449 through 469
      removed outlier: 4.242A  pdb=" N   SER A 453 " --> pdb=" O   ASP A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 481
      removed outlier: 4.985A  pdb=" N   GLN A 475 " --> pdb=" O   ALA A 471 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   THR A 476 " --> pdb=" O   THR A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 514
    Processing helix  chain 'A' and resid 515 through 519
      removed outlier: 3.881A  pdb=" N   ALA A 519 " --> pdb=" O   ARG A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 531
    Processing helix  chain 'A' and resid 571 through 600
    Processing helix  chain 'A' and resid 604 through 619
    Processing helix  chain 'A' and resid 627 through 633
      removed outlier: 3.964A  pdb=" N   LEU A 631 " --> pdb=" O   LEU A 627 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   LYS A 633 " --> pdb=" O   ASP A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 652
    Processing helix  chain 'A' and resid 653 through 657
      removed outlier: 4.504A  pdb=" N   LYS A 656 " --> pdb=" O   SER A 653 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 676
    Processing helix  chain 'A' and resid 677 through 703
      removed outlier: 3.942A  pdb=" N   GLU A 681 " --> pdb=" O   HIS A 677 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   VAL A 693 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
      Proline residue:  A 694  - end of helix
      removed outlier: 4.093A  pdb=" N   PHE A 699 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 755
      removed outlier: 3.657A  pdb=" N   ALA A 731 " --> pdb=" O   LYS A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 756 through 760
      removed outlier: 4.063A  pdb=" N   ILE A 759 " --> pdb=" O   ARG A 756 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 780
    Processing helix  chain 'A' and resid 797 through 811
      removed outlier: 3.676A  pdb=" N   ARG A 803 " --> pdb=" O   VAL A 799 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ARG A 806 " --> pdb=" O   PHE A 802 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ARG A 809 " --> pdb=" O   LEU A 805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 854
      Proline residue:  A 819  - end of helix
      removed outlier: 3.643A  pdb=" N   LYS A 852 " --> pdb=" O   GLU A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 857
      No H-bonds generated for 'chain 'A' and resid 855 through 857'
    Processing helix  chain 'A' and resid 860 through 889
    Processing helix  chain 'A' and resid 889 through 919
    Processing helix  chain 'A' and resid 923 through 942
      removed outlier: 3.644A  pdb=" N   MET A 942 " --> pdb=" O   MET A 938 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 959
    Processing helix  chain 'A' and resid 960 through 964
      removed outlier: 3.525A  pdb=" N   ALA A 964 " --> pdb=" O   SER A 961 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 977
    Processing helix  chain 'A' and resid 1043 through 1050
    Processing helix  chain 'A' and resid 1070 through 1080
    Processing helix  chain 'A' and resid 1085 through 1108
      Proline residue:  A1101  - end of helix
    Processing helix  chain 'A' and resid 1113 through 1123
    Processing helix  chain 'A' and resid 1179 through 1183
    Processing helix  chain 'B' and resid 76 through 95
      removed outlier: 3.566A  pdb=" N   PHE B  80 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 120
      removed outlier: 3.986A  pdb=" N   VAL B 105 " --> pdb=" O   PRO B 101 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ASN B 119 " --> pdb=" O   VAL B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 132
      removed outlier: 4.644A  pdb=" N   ASP B 129 " --> pdb=" O   GLU B 125 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   VAL B 130 " --> pdb=" O   HIS B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 153
      Proline residue:  B 144  - end of helix
    Processing helix  chain 'B' and resid 155 through 162
    Processing helix  chain 'B' and resid 162 through 188
      removed outlier: 3.574A  pdb=" N   GLY B 173 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 207
      removed outlier: 3.564A  pdb=" N   ALA B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 221
      removed outlier: 3.924A  pdb=" N   LEU B 216 " --> pdb=" O   ALA B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 254
      removed outlier: 3.566A  pdb=" N   GLY B 227 " --> pdb=" O   SER B 223 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   THR B 228 " --> pdb=" O   LYS B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 273
    Processing helix  chain 'B' and resid 273 through 291
    Processing helix  chain 'B' and resid 296 through 317
    Processing helix  chain 'B' and resid 322 through 337
    Processing helix  chain 'B' and resid 338 through 341
    Processing helix  chain 'B' and resid 342 through 376
      removed outlier: 3.637A  pdb=" N   ARG B 351 " --> pdb=" O   VAL B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 380
    Processing helix  chain 'B' and resid 381 through 412
      removed outlier: 3.835A  pdb=" N   TRP B 385 " --> pdb=" O   ASP B 381 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   PHE B 386 " --> pdb=" O   LYS B 382 " (cutoff:3.500A)
      Proline residue:  B 408  - end of helix
      removed outlier: 3.997A  pdb=" N   ARG B 412 " --> pdb=" O   PRO B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 428
    Processing helix  chain 'B' and resid 432 through 447
    Processing helix  chain 'B' and resid 449 through 469
      removed outlier: 4.242A  pdb=" N   SER B 453 " --> pdb=" O   ASP B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 481
      removed outlier: 4.986A  pdb=" N   GLN B 475 " --> pdb=" O   ALA B 471 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   THR B 476 " --> pdb=" O   THR B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 514
    Processing helix  chain 'B' and resid 515 through 519
      removed outlier: 3.880A  pdb=" N   ALA B 519 " --> pdb=" O   ARG B 516 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 522 through 531
    Processing helix  chain 'B' and resid 571 through 600
    Processing helix  chain 'B' and resid 604 through 619
    Processing helix  chain 'B' and resid 627 through 633
      removed outlier: 3.964A  pdb=" N   LEU B 631 " --> pdb=" O   LEU B 627 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   LYS B 633 " --> pdb=" O   ASP B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 639 through 652
    Processing helix  chain 'B' and resid 653 through 657
      removed outlier: 4.504A  pdb=" N   LYS B 656 " --> pdb=" O   SER B 653 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 672 through 676
    Processing helix  chain 'B' and resid 677 through 703
      removed outlier: 3.942A  pdb=" N   GLU B 681 " --> pdb=" O   HIS B 677 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   VAL B 693 " --> pdb=" O   VAL B 689 " (cutoff:3.500A)
      Proline residue:  B 694  - end of helix
      removed outlier: 4.093A  pdb=" N   PHE B 699 " --> pdb=" O   ILE B 695 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 726 through 755
      removed outlier: 3.657A  pdb=" N   ALA B 731 " --> pdb=" O   LYS B 727 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 756 through 760
      removed outlier: 4.062A  pdb=" N   ILE B 759 " --> pdb=" O   ARG B 756 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 761 through 780
    Processing helix  chain 'B' and resid 797 through 811
      removed outlier: 3.676A  pdb=" N   ARG B 803 " --> pdb=" O   VAL B 799 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ARG B 806 " --> pdb=" O   PHE B 802 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ARG B 809 " --> pdb=" O   LEU B 805 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 813 through 854
      Proline residue:  B 819  - end of helix
      removed outlier: 3.643A  pdb=" N   LYS B 852 " --> pdb=" O   GLU B 848 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 855 through 857
      No H-bonds generated for 'chain 'B' and resid 855 through 857'
    Processing helix  chain 'B' and resid 860 through 889
    Processing helix  chain 'B' and resid 889 through 919
    Processing helix  chain 'B' and resid 923 through 942
      removed outlier: 3.643A  pdb=" N   MET B 942 " --> pdb=" O   MET B 938 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 952 through 959
    Processing helix  chain 'B' and resid 960 through 964
      removed outlier: 3.525A  pdb=" N   ALA B 964 " --> pdb=" O   SER B 961 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 966 through 977
    Processing helix  chain 'B' and resid 1043 through 1050
    Processing helix  chain 'B' and resid 1070 through 1080
    Processing helix  chain 'B' and resid 1085 through 1108
      Proline residue:  B1101  - end of helix
    Processing helix  chain 'B' and resid 1113 through 1123
    Processing helix  chain 'B' and resid 1179 through 1183
    Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982
      removed outlier: 6.366A  pdb=" N   GLN A1064 " --> pdb=" O   VAL A1002 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989
      removed outlier: 6.718A  pdb=" N   VAL A 987 " --> pdb=" O   CYS A1059 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   CYS A1059 " --> pdb=" O   VAL A 987 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   VAL A 989 " --> pdb=" O   VAL A1057 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1127
      removed outlier: 4.771A  pdb=" N   LEU A1186 " --> pdb=" O   VAL A1127 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   ARG A1185 " --> pdb=" O   ILE A1148 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1134 through 1136
      removed outlier: 3.644A  pdb=" N   ALA A1152 " --> pdb=" O   ILE A1161 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 978 through 982
      removed outlier: 6.366A  pdb=" N   GLN B1064 " --> pdb=" O   VAL B1002 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 987 through 989
      removed outlier: 6.718A  pdb=" N   VAL B 987 " --> pdb=" O   CYS B1059 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   CYS B1059 " --> pdb=" O   VAL B 987 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   VAL B 989 " --> pdb=" O   VAL B1057 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1125 through 1127
      removed outlier: 4.770A  pdb=" N   LEU B1186 " --> pdb=" O   VAL B1127 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   ARG B1185 " --> pdb=" O   ILE B1148 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1134 through 1136
      removed outlier: 3.644A  pdb=" N   ALA B1152 " --> pdb=" O   ILE B1161 " (cutoff:3.500A)

    1208 hydrogen bonds defined for protein.
    3534 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: 5.69

  Time building geometry restraints manager: 4.79 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4054
        1.33 -     1.46: 3362
        1.46 -     1.58: 8922
        1.58 -     1.70: 0
        1.70 -     1.83: 154
  Bond restraints: 16492
  Sorted by residual:
  bond pdb=" C   GLN B 624 "
       pdb=" O   GLN B 624 "
    ideal  model  delta    sigma   weight residual
    1.235  1.210  0.025 1.19e-02 7.06e+03 4.50e+00
  bond pdb=" N   ALA B 619 "
       pdb=" CA  ALA B 619 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.35e-02 5.49e+03 4.36e+00
  bond pdb=" C   GLN A 624 "
       pdb=" O   GLN A 624 "
    ideal  model  delta    sigma   weight residual
    1.235  1.211  0.025 1.19e-02 7.06e+03 4.33e+00
  bond pdb=" N   ALA A 619 "
       pdb=" CA  ALA A 619 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.35e-02 5.49e+03 4.23e+00
  bond pdb=" N   ASP A 623 "
       pdb=" CA  ASP A 623 "
    ideal  model  delta    sigma   weight residual
    1.457  1.483 -0.025 1.29e-02 6.01e+03 3.84e+00
  ... (remaining 16487 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 21940
        1.69 -     3.37: 357
        3.37 -     5.06: 55
        5.06 -     6.74: 8
        6.74 -     8.43: 4
  Bond angle restraints: 22364
  Sorted by residual:
  angle pdb=" CA  GLN A 624 "
        pdb=" C   GLN A 624 "
        pdb=" O   GLN A 624 "
      ideal   model   delta    sigma   weight residual
     120.54  116.32    4.22 1.04e+00 9.25e-01 1.65e+01
  angle pdb=" CA  GLN B 624 "
        pdb=" C   GLN B 624 "
        pdb=" O   GLN B 624 "
      ideal   model   delta    sigma   weight residual
     120.54  116.33    4.21 1.04e+00 9.25e-01 1.64e+01
  angle pdb=" CA  ASP B 620 "
        pdb=" C   ASP B 620 "
        pdb=" O   ASP B 620 "
      ideal   model   delta    sigma   weight residual
     121.32  117.13    4.19 1.16e+00 7.43e-01 1.30e+01
  angle pdb=" CA  ASP A 620 "
        pdb=" C   ASP A 620 "
        pdb=" O   ASP A 620 "
      ideal   model   delta    sigma   weight residual
     121.32  117.16    4.16 1.16e+00 7.43e-01 1.28e+01
  angle pdb=" CG  MET B1073 "
        pdb=" SD  MET B1073 "
        pdb=" CE  MET B1073 "
      ideal   model   delta    sigma   weight residual
     100.90  108.24   -7.34 2.20e+00 2.07e-01 1.11e+01
  ... (remaining 22359 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.44: 8989
       16.44 -    32.88: 649
       32.88 -    49.31: 168
       49.31 -    65.75: 24
       65.75 -    82.19: 18
  Dihedral angle restraints: 9848
    sinusoidal: 3896
      harmonic: 5952
  Sorted by residual:
  dihedral pdb=" CA  PRO A 210 "
           pdb=" C   PRO A 210 "
           pdb=" N   VAL A 211 "
           pdb=" CA  VAL A 211 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.80  -20.20     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  PRO B 210 "
           pdb=" C   PRO B 210 "
           pdb=" N   VAL B 211 "
           pdb=" CA  VAL B 211 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.81  -20.19     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  MET A 154 "
           pdb=" C   MET A 154 "
           pdb=" N   ASP A 155 "
           pdb=" CA  ASP A 155 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.85   20.15     0      5.00e+00 4.00e-02 1.62e+01
  ... (remaining 9845 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1649
       0.027 -    0.055: 583
       0.055 -    0.082: 305
       0.082 -    0.109: 121
       0.109 -    0.136: 30
  Chirality restraints: 2688
  Sorted by residual:
  chirality pdb=" CA  ILE A 948 "
            pdb=" N   ILE A 948 "
            pdb=" C   ILE A 948 "
            pdb=" CB  ILE A 948 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.64e-01
  chirality pdb=" CA  ILE B 948 "
            pdb=" N   ILE B 948 "
            pdb=" C   ILE B 948 "
            pdb=" CB  ILE B 948 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.54e-01
  chirality pdb=" CA  ILE B1068 "
            pdb=" N   ILE B1068 "
            pdb=" C   ILE B1068 "
            pdb=" CB  ILE B1068 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 2685 not shown)

  Planarity restraints: 2750
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 571 "   -0.033 5.00e-02 4.00e+02   5.00e-02 4.00e+00
        pdb=" N   PRO A 572 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 572 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 572 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 571 "    0.033 5.00e-02 4.00e+02   4.99e-02 3.98e+00
        pdb=" N   PRO B 572 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO B 572 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 572 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 275 "   -0.029 5.00e-02 4.00e+02   4.31e-02 2.97e+00
        pdb=" N   PRO A 276 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 276 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 276 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 2747 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 2207
        2.75 -     3.29: 17035
        3.29 -     3.83: 26404
        3.83 -     4.36: 30483
        4.36 -     4.90: 54307
  Nonbonded interactions: 130436
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 923 "
            pdb=" N   GLU A 924 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" OD1 ASP B 923 "
            pdb=" N   GLU B 924 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" O   ALA A1140 "
            pdb=" OG1 THR A1141 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   ALA B1140 "
            pdb=" OG1 THR B1141 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OD1 ASN B 237 "
            pdb=" N   ASP B 238 "
     model   vdw
     2.306 3.120
  ... (remaining 130431 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.710
  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:          0.650
  Check model and map are aligned:         0.120
  Set scattering table:                    0.140
  Process input model:                     46.990
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7060
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16492  Z= 0.153
  Angle     :  0.559   8.429  22364  Z= 0.314
  Chirality :  0.039   0.136   2688
  Planarity :  0.004   0.050   2750
  Dihedral  : 12.911  82.188   5988
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  5.23 %
    Favored  : 94.55 %
  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:  1.86 (0.19), residues: 2022
  helix:  1.85 (0.14), residues: 1442
  sheet:  0.17 (0.61), residues: 76
  loop : -0.34 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 419 
 HIS   0.005   0.001   HIS A1120 
 PHE   0.012   0.001   PHE A 769 
 TYR   0.014   0.001   TYR A 737 
 ARG   0.006   0.001   ARG A 573 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11144 ( 1208)
  hydrogen bonds       : angle       5.16122 ( 3534)
  covalent geometry    : bond        0.00320 (16492)
  covalent geometry    : angle       0.55945 (22364)

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

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

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  533 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 529
  time to evaluate  : 1.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 LYS cc_start: 0.7816 (ttpt) cc_final: 0.7528 (ttpt)
REVERT: A  132 HIS cc_start: 0.7080 (m-70) cc_final: 0.6727 (m-70)
REVERT: A  160 MET cc_start: 0.7337 (mmt) cc_final: 0.6957 (mmm)
REVERT: A  163 PHE cc_start: 0.7576 (t80) cc_final: 0.7260 (t80)
REVERT: A  164 SER cc_start: 0.7963 (m) cc_final: 0.7696 (p)
REVERT: A  233 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7098 (tt0)
REVERT: A  250 LYS cc_start: 0.7397 (mttt) cc_final: 0.7148 (mttt)
REVERT: A  300 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7625 (mt-10)
REVERT: A  316 ASP cc_start: 0.7776 (t0) cc_final: 0.7424 (m-30)
REVERT: A  319 LEU cc_start: 0.8222 (mt) cc_final: 0.7981 (mp)
REVERT: A  320 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7337 (mt-10)
REVERT: A  337 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7189 (mm-30)
REVERT: A  375 LYS cc_start: 0.7867 (mttt) cc_final: 0.7474 (mttt)
REVERT: A  383 MET cc_start: 0.7343 (tpp) cc_final: 0.6656 (mmm)
REVERT: A  485 ASP cc_start: 0.7454 (m-30) cc_final: 0.7228 (p0)
REVERT: A  511 MET cc_start: 0.7165 (tmm) cc_final: 0.6732 (ttp)
REVERT: A  516 ARG cc_start: 0.8065 (ptm160) cc_final: 0.7853 (ptm160)
REVERT: A  580 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6456 (tp30)
REVERT: A  633 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7458 (mtmm)
REVERT: A  640 ILE cc_start: 0.7070 (mt) cc_final: 0.6416 (tt)
REVERT: A  644 LEU cc_start: 0.7025 (mt) cc_final: 0.6559 (mp)
REVERT: A  648 LEU cc_start: 0.6689 (mt) cc_final: 0.6487 (mp)
REVERT: A  777 ASP cc_start: 0.3050 (m-30) cc_final: 0.2629 (t70)
REVERT: A  810 MET cc_start: 0.4995 (ptp) cc_final: 0.4572 (ptp)
REVERT: A  837 TYR cc_start: 0.7784 (m-80) cc_final: 0.7553 (m-80)
REVERT: A  847 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6624 (mm-30)
REVERT: A  877 GLN cc_start: 0.7549 (tt0) cc_final: 0.7141 (tt0)
REVERT: A  903 ARG cc_start: 0.7564 (mtm-85) cc_final: 0.7250 (ttm-80)
REVERT: A  925 MET cc_start: 0.6125 (ppp) cc_final: 0.5885 (ppp)
REVERT: A  939 LYS cc_start: 0.7799 (tttt) cc_final: 0.7562 (tttt)
REVERT: A  966 ASP cc_start: 0.7729 (t0) cc_final: 0.7289 (t0)
REVERT: A  994 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7175 (mt-10)
REVERT: A 1003 SER cc_start: 0.7831 (t) cc_final: 0.7501 (t)
REVERT: A 1007 LYS cc_start: 0.7572 (tttt) cc_final: 0.7055 (tttp)
REVERT: A 1033 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7078 (mt-10)
REVERT: A 1037 THR cc_start: 0.7705 (t) cc_final: 0.7491 (m)
REVERT: A 1044 GLU cc_start: 0.5881 (mt-10) cc_final: 0.5393 (mt-10)
REVERT: A 1051 LYS cc_start: 0.8520 (mttm) cc_final: 0.7998 (mttm)
REVERT: A 1054 ASN cc_start: 0.8297 (t0) cc_final: 0.7708 (t0)
REVERT: A 1073 MET cc_start: 0.7226 (mmp) cc_final: 0.7024 (mmm)
REVERT: A 1107 MET cc_start: 0.5770 (mtt) cc_final: 0.5531 (mpp)
REVERT: A 1122 GLU cc_start: 0.7528 (tp30) cc_final: 0.7316 (tp30)
REVERT: A 1123 ARG cc_start: 0.7644 (ttm170) cc_final: 0.7076 (ttp80)
REVERT: A 1125 TYR cc_start: 0.6141 (p90) cc_final: 0.5810 (p90)
REVERT: A 1191 ASN cc_start: 0.7343 (t0) cc_final: 0.7137 (p0)
REVERT: B   91 SER cc_start: 0.7829 (m) cc_final: 0.7429 (p)
REVERT: B   96 LYS cc_start: 0.7867 (ttpt) cc_final: 0.7551 (ttpt)
REVERT: B   97 LYS cc_start: 0.7935 (ptmt) cc_final: 0.7673 (ptmt)
REVERT: B  149 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7317 (tm-30)
REVERT: B  150 SER cc_start: 0.7821 (t) cc_final: 0.7472 (m)
REVERT: B  160 MET cc_start: 0.7593 (mmt) cc_final: 0.7257 (mmm)
REVERT: B  161 ARG cc_start: 0.7387 (mtm-85) cc_final: 0.7181 (mtm-85)
REVERT: B  164 SER cc_start: 0.7832 (m) cc_final: 0.7616 (p)
REVERT: B  233 GLU cc_start: 0.7281 (tm-30) cc_final: 0.7028 (tt0)
REVERT: B  250 LYS cc_start: 0.7401 (mttt) cc_final: 0.7044 (mttp)
REVERT: B  259 SER cc_start: 0.8037 (m) cc_final: 0.7800 (t)
REVERT: B  300 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7650 (mt-10)
REVERT: B  320 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7393 (mt-10)
REVERT: B  337 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7210 (mm-30)
REVERT: B  355 MET cc_start: 0.7787 (tmm) cc_final: 0.7451 (ttp)
REVERT: B  383 MET cc_start: 0.7264 (tpp) cc_final: 0.6519 (mmm)
REVERT: B  387 TYR cc_start: 0.7641 (m-10) cc_final: 0.7426 (m-10)
REVERT: B  443 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7173 (tm-30)
REVERT: B  475 GLN cc_start: 0.7628 (tp40) cc_final: 0.7419 (tt0)
REVERT: B  486 ILE cc_start: 0.8220 (mp) cc_final: 0.7954 (mm)
REVERT: B  580 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6296 (tp30)
REVERT: B  591 LYS cc_start: 0.7236 (mtmt) cc_final: 0.6969 (mtpp)
REVERT: B  621 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6045 (mt-10)
REVERT: B  632 LYS cc_start: 0.7338 (ttmm) cc_final: 0.7098 (ttmm)
REVERT: B  633 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7547 (mmtm)
REVERT: B  634 SER cc_start: 0.8444 (m) cc_final: 0.8001 (t)
REVERT: B  635 TRP cc_start: 0.7385 (p90) cc_final: 0.7021 (p90)
REVERT: B  678 MET cc_start: 0.7041 (mmm) cc_final: 0.6839 (mmm)
REVERT: B  697 MET cc_start: 0.6135 (ttt) cc_final: 0.5865 (ttt)
REVERT: B  777 ASP cc_start: 0.3459 (m-30) cc_final: 0.2638 (t70)
REVERT: B  810 MET cc_start: 0.5081 (ptp) cc_final: 0.4529 (ptp)
REVERT: B  847 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6719 (mm-30)
REVERT: B  877 GLN cc_start: 0.7585 (tt0) cc_final: 0.7095 (tt0)
REVERT: B  880 LYS cc_start: 0.7226 (ttpp) cc_final: 0.6938 (tttp)
REVERT: B  903 ARG cc_start: 0.7411 (mtm-85) cc_final: 0.7085 (ttm-80)
REVERT: B  966 ASP cc_start: 0.7552 (t0) cc_final: 0.7193 (t0)
REVERT: B  990 ARG cc_start: 0.7182 (mtt-85) cc_final: 0.6898 (mtp85)
REVERT: B  994 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7124 (mt-10)
REVERT: B 1003 SER cc_start: 0.7835 (t) cc_final: 0.7448 (t)
REVERT: B 1007 LYS cc_start: 0.7545 (tttt) cc_final: 0.7235 (tttp)
REVERT: B 1037 THR cc_start: 0.7762 (t) cc_final: 0.7543 (m)
REVERT: B 1051 LYS cc_start: 0.8442 (mttm) cc_final: 0.7938 (mttm)
REVERT: B 1054 ASN cc_start: 0.8457 (t0) cc_final: 0.7991 (t0)
REVERT: B 1064 GLN cc_start: 0.7620 (mt0) cc_final: 0.7362 (mt0)
REVERT: B 1115 GLU cc_start: 0.7495 (tt0) cc_final: 0.7236 (tt0)
REVERT: B 1123 ARG cc_start: 0.7721 (ttm170) cc_final: 0.7380 (ttp80)
REVERT: B 1125 TYR cc_start: 0.6110 (p90) cc_final: 0.5885 (p90)
REVERT: B 1191 ASN cc_start: 0.7324 (t0) cc_final: 0.7112 (p0)
  outliers start: 4
  outliers final: 3
  residues processed: 533
  average time/residue: 0.3305
  time to fit residues: 246.4761
Evaluate side-chains
  450 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 447
  time to evaluate  : 1.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  622 LYS
Chi-restraints excluded: chain B residue  622 LYS
Chi-restraints excluded: chain B residue 1134 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 172 optimal weight:    3.9990
   chunk 154 optimal weight:    0.6980
   chunk 85 optimal weight:    0.3980
   chunk 52 optimal weight:    8.9990
   chunk 104 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 159 optimal weight:    5.9990
   chunk 61 optimal weight:    8.9990
   chunk 97 optimal weight:    2.9990
   chunk 119 optimal weight:    0.6980
   chunk 185 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN
A 624 GLN
A 981 HIS
** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 421 ASN
B 624 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.154240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.130018 restraints weight = 22016.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 1.62
r_work: 0.3460 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  16492  Z= 0.186
  Angle     :  0.568   8.560  22364  Z= 0.305
  Chirality :  0.043   0.168   2688
  Planarity :  0.004   0.049   2750
  Dihedral  :  4.352  38.332   2194
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 10.97 %
    Favored  : 87.16 %
  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:  2.12 (0.19), residues: 2022
  helix:  1.98 (0.13), residues: 1460
  sheet:  0.26 (0.56), residues: 92
  loop : -0.10 (0.30), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 962 
 HIS   0.007   0.001   HIS B1120 
 PHE   0.023   0.002   PHE B 769 
 TYR   0.017   0.001   TYR A 984 
 ARG   0.010   0.001   ARG B 856 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04982 ( 1208)
  hydrogen bonds       : angle       4.32674 ( 3534)
  covalent geometry    : bond        0.00433 (16492)
  covalent geometry    : angle       0.56840 (22364)

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

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

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  495 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 462
  time to evaluate  : 1.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7987 (ttpt)
REVERT: A  163 PHE cc_start: 0.8292 (t80) cc_final: 0.7975 (t80)
REVERT: A  250 LYS cc_start: 0.8614 (mttt) cc_final: 0.8394 (mttt)
REVERT: A  289 PHE cc_start: 0.8290 (m-80) cc_final: 0.8042 (m-80)
REVERT: A  300 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7671 (mt-10)
REVERT: A  383 MET cc_start: 0.8315 (tpp) cc_final: 0.7965 (mmm)
REVERT: A  419 TRP cc_start: 0.8574 (p-90) cc_final: 0.8284 (p-90)
REVERT: A  511 MET cc_start: 0.8119 (tmm) cc_final: 0.7620 (ttp)
REVERT: A  580 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7485 (tp30)
REVERT: A  591 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8229 (mtpp)
REVERT: A  608 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7968 (tp)
REVERT: A  621 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7342 (mt-10)
REVERT: A  622 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7415 (mtpm)
REVERT: A  628 VAL cc_start: 0.8512 (p) cc_final: 0.7943 (p)
REVERT: A  633 LYS cc_start: 0.8379 (mtmm) cc_final: 0.8100 (mtmm)
REVERT: A  640 ILE cc_start: 0.8145 (mt) cc_final: 0.7586 (tt)
REVERT: A  644 LEU cc_start: 0.8298 (mt) cc_final: 0.7955 (mp)
REVERT: A  678 MET cc_start: 0.7201 (mmm) cc_final: 0.6551 (tmm)
REVERT: A  777 ASP cc_start: 0.4879 (m-30) cc_final: 0.3794 (t0)
REVERT: A  810 MET cc_start: 0.5653 (ptp) cc_final: 0.5176 (ptp)
REVERT: A  828 LYS cc_start: 0.8442 (mttt) cc_final: 0.8120 (mmmm)
REVERT: A  847 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7378 (mm-30)
REVERT: A  877 GLN cc_start: 0.8423 (tt0) cc_final: 0.8025 (tt0)
REVERT: A  938 MET cc_start: 0.8353 (tpp) cc_final: 0.8152 (mtp)
REVERT: A 1003 SER cc_start: 0.8672 (t) cc_final: 0.8413 (t)
REVERT: A 1007 LYS cc_start: 0.8554 (tttt) cc_final: 0.8323 (tttt)
REVERT: A 1037 THR cc_start: 0.8431 (t) cc_final: 0.8156 (m)
REVERT: A 1044 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7008 (mt-10)
REVERT: A 1054 ASN cc_start: 0.8367 (t0) cc_final: 0.7977 (t0)
REVERT: A 1061 THR cc_start: 0.8701 (t) cc_final: 0.8473 (t)
REVERT: A 1125 TYR cc_start: 0.7625 (p90) cc_final: 0.7424 (p90)
REVERT: A 1134 PHE cc_start: 0.6665 (OUTLIER) cc_final: 0.6393 (p90)
REVERT: B   96 LYS cc_start: 0.8272 (ttpt) cc_final: 0.8036 (ttpt)
REVERT: B  154 MET cc_start: 0.8370 (mmm) cc_final: 0.7788 (mmm)
REVERT: B  160 MET cc_start: 0.7870 (mmt) cc_final: 0.7592 (mmm)
REVERT: B  205 MET cc_start: 0.8077 (mmm) cc_final: 0.7630 (mmm)
REVERT: B  233 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7448 (tt0)
REVERT: B  250 LYS cc_start: 0.8664 (mttt) cc_final: 0.8369 (mttm)
REVERT: B  300 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7635 (mt-10)
REVERT: B  355 MET cc_start: 0.8433 (tmm) cc_final: 0.7832 (ttp)
REVERT: B  383 MET cc_start: 0.8328 (tpp) cc_final: 0.7713 (mmm)
REVERT: B  387 TYR cc_start: 0.8473 (m-10) cc_final: 0.8179 (m-10)
REVERT: B  580 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7340 (tp30)
REVERT: B  590 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7861 (mt-10)
REVERT: B  591 LYS cc_start: 0.8457 (mtmt) cc_final: 0.8255 (mtpp)
REVERT: B  621 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7351 (mt-10)
REVERT: B  628 VAL cc_start: 0.8631 (p) cc_final: 0.8152 (p)
REVERT: B  632 LYS cc_start: 0.8453 (ttmm) cc_final: 0.7992 (ttmm)
REVERT: B  633 LYS cc_start: 0.8448 (mtmm) cc_final: 0.8194 (mmtp)
REVERT: B  634 SER cc_start: 0.8715 (m) cc_final: 0.8304 (t)
REVERT: B  640 ILE cc_start: 0.8292 (mt) cc_final: 0.8043 (tt)
REVERT: B  697 MET cc_start: 0.5874 (ttt) cc_final: 0.5562 (ttt)
REVERT: B  810 MET cc_start: 0.5686 (ptp) cc_final: 0.5072 (ptp)
REVERT: B  847 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7372 (mm-30)
REVERT: B  877 GLN cc_start: 0.8435 (tt0) cc_final: 0.8031 (tt0)
REVERT: B  881 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7511 (mt-10)
REVERT: B  967 MET cc_start: 0.7804 (mmm) cc_final: 0.7591 (mmm)
REVERT: B  969 LEU cc_start: 0.7991 (tp) cc_final: 0.7778 (tp)
REVERT: B 1003 SER cc_start: 0.8678 (t) cc_final: 0.8462 (t)
REVERT: B 1007 LYS cc_start: 0.8589 (tttt) cc_final: 0.8211 (tttm)
REVERT: B 1037 THR cc_start: 0.8456 (t) cc_final: 0.8156 (m)
REVERT: B 1044 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7061 (mt-10)
REVERT: B 1054 ASN cc_start: 0.8405 (t0) cc_final: 0.8026 (t0)
REVERT: B 1058 THR cc_start: 0.8472 (m) cc_final: 0.8220 (p)
REVERT: B 1060 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7574 (mm-30)
REVERT: B 1122 GLU cc_start: 0.7683 (tp30) cc_final: 0.7262 (tp30)
REVERT: B 1134 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.6161 (p90)
  outliers start: 33
  outliers final: 13
  residues processed: 474
  average time/residue: 0.3106
  time to fit residues: 211.5606
Evaluate side-chains
  453 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 436
  time to evaluate  : 1.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  613 GLN
Chi-restraints excluded: chain A residue  622 LYS
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  852 LYS
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  926 GLU
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue 1134 PHE
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  613 GLN
Chi-restraints excluded: chain B residue  916 LEU
Chi-restraints excluded: chain B residue  926 GLU
Chi-restraints excluded: chain B residue  973 ILE
Chi-restraints excluded: chain B residue 1134 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 125 optimal weight:    2.9990
   chunk 160 optimal weight:   20.0000
   chunk 173 optimal weight:    2.9990
   chunk 167 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 139 optimal weight:    1.9990
   chunk 117 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 175 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 981 HIS
** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 HIS
B 140 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.152583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.128334 restraints weight = 21952.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 1.60
r_work: 0.3440 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  16492  Z= 0.203
  Angle     :  0.554   9.167  22364  Z= 0.297
  Chirality :  0.044   0.164   2688
  Planarity :  0.004   0.063   2750
  Dihedral  :  4.215  38.792   2190
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 13.75 %
    Favored  : 83.81 %
  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:  1.95 (0.19), residues: 2022
  helix:  1.84 (0.13), residues: 1460
  sheet:  0.41 (0.58), residues: 86
  loop : -0.18 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 278 
 HIS   0.007   0.001   HIS B1120 
 PHE   0.023   0.002   PHE B 769 
 TYR   0.017   0.001   TYR B1009 
 ARG   0.008   0.001   ARG A1123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04927 ( 1208)
  hydrogen bonds       : angle       4.25529 ( 3534)
  covalent geometry    : bond        0.00479 (16492)
  covalent geometry    : angle       0.55417 (22364)

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

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

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  478 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 435
  time to evaluate  : 1.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 PHE cc_start: 0.8211 (t80) cc_final: 0.7873 (t80)
REVERT: A  205 MET cc_start: 0.7980 (mmm) cc_final: 0.7284 (mmt)
REVERT: A  289 PHE cc_start: 0.8331 (m-10) cc_final: 0.8080 (m-80)
REVERT: A  300 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7660 (mt-10)
REVERT: A  383 MET cc_start: 0.8305 (tpp) cc_final: 0.8027 (mmm)
REVERT: A  419 TRP cc_start: 0.8591 (p-90) cc_final: 0.8357 (p-90)
REVERT: A  475 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7991 (mm-40)
REVERT: A  499 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7632 (ttm170)
REVERT: A  511 MET cc_start: 0.8169 (tmm) cc_final: 0.7661 (ttp)
REVERT: A  516 ARG cc_start: 0.8051 (ptm-80) cc_final: 0.7827 (ptm160)
REVERT: A  580 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7549 (tp30)
REVERT: A  591 LYS cc_start: 0.8512 (mtmt) cc_final: 0.8254 (mtpp)
REVERT: A  608 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8061 (tp)
REVERT: A  621 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7382 (mt-10)
REVERT: A  623 ASP cc_start: 0.7490 (t0) cc_final: 0.7256 (t0)
REVERT: A  628 VAL cc_start: 0.8482 (p) cc_final: 0.7839 (p)
REVERT: A  633 LYS cc_start: 0.8434 (mtmm) cc_final: 0.8135 (mtmm)
REVERT: A  640 ILE cc_start: 0.8174 (mt) cc_final: 0.7730 (tt)
REVERT: A  644 LEU cc_start: 0.8329 (mt) cc_final: 0.8065 (mp)
REVERT: A  678 MET cc_start: 0.7177 (mmm) cc_final: 0.6566 (tmm)
REVERT: A  777 ASP cc_start: 0.4985 (m-30) cc_final: 0.4314 (m-30)
REVERT: A  810 MET cc_start: 0.5605 (ptp) cc_final: 0.5220 (ptp)
REVERT: A  828 LYS cc_start: 0.8475 (mttt) cc_final: 0.8158 (mmmm)
REVERT: A  847 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7371 (mm-30)
REVERT: A  877 GLN cc_start: 0.8493 (tt0) cc_final: 0.8086 (tt0)
REVERT: A  938 MET cc_start: 0.8384 (tpp) cc_final: 0.8113 (mtp)
REVERT: A  963 LEU cc_start: 0.8346 (mt) cc_final: 0.8129 (mt)
REVERT: A  989 VAL cc_start: 0.9016 (p) cc_final: 0.8676 (m)
REVERT: A 1003 SER cc_start: 0.8692 (t) cc_final: 0.8321 (m)
REVERT: A 1007 LYS cc_start: 0.8511 (tttt) cc_final: 0.8063 (tttp)
REVERT: A 1033 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7376 (mt-10)
REVERT: A 1037 THR cc_start: 0.8385 (t) cc_final: 0.8144 (m)
REVERT: A 1044 GLU cc_start: 0.7602 (mt-10) cc_final: 0.6955 (mt-10)
REVERT: A 1054 ASN cc_start: 0.8315 (t0) cc_final: 0.7918 (t0)
REVERT: A 1112 TRP cc_start: 0.5357 (OUTLIER) cc_final: 0.5047 (m-10)
REVERT: A 1134 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.6369 (p90)
REVERT: B   96 LYS cc_start: 0.8332 (ttpt) cc_final: 0.8082 (ttpt)
REVERT: B  160 MET cc_start: 0.7894 (mmt) cc_final: 0.7634 (mmm)
REVERT: B  233 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7467 (tt0)
REVERT: B  250 LYS cc_start: 0.8620 (mttt) cc_final: 0.8357 (mttp)
REVERT: B  300 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7576 (mt-10)
REVERT: B  339 THR cc_start: 0.8624 (m) cc_final: 0.8404 (p)
REVERT: B  355 MET cc_start: 0.8484 (tmm) cc_final: 0.7875 (ttp)
REVERT: B  383 MET cc_start: 0.8315 (tpp) cc_final: 0.7853 (mmm)
REVERT: B  387 TYR cc_start: 0.8512 (m-10) cc_final: 0.8145 (m-10)
REVERT: B  407 SER cc_start: 0.7911 (t) cc_final: 0.7575 (p)
REVERT: B  580 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7399 (tp30)
REVERT: B  590 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7930 (mt-10)
REVERT: B  591 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8281 (mtpp)
REVERT: B  621 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7480 (mt-10)
REVERT: B  628 VAL cc_start: 0.8621 (p) cc_final: 0.8284 (p)
REVERT: B  632 LYS cc_start: 0.8487 (ttmm) cc_final: 0.7891 (ttmm)
REVERT: B  633 LYS cc_start: 0.8504 (mtmm) cc_final: 0.8285 (mmtm)
REVERT: B  640 ILE cc_start: 0.8304 (mt) cc_final: 0.8098 (tt)
REVERT: B  697 MET cc_start: 0.5819 (ttt) cc_final: 0.5504 (ttt)
REVERT: B  810 MET cc_start: 0.5605 (ptp) cc_final: 0.5039 (ptp)
REVERT: B  847 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7489 (mm-30)
REVERT: B  849 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7620 (mt-10)
REVERT: B  877 GLN cc_start: 0.8512 (tt0) cc_final: 0.8053 (tt0)
REVERT: B  967 MET cc_start: 0.7646 (mmm) cc_final: 0.7364 (mmm)
REVERT: B 1007 LYS cc_start: 0.8565 (tttt) cc_final: 0.8327 (tttp)
REVERT: B 1037 THR cc_start: 0.8302 (t) cc_final: 0.8084 (m)
REVERT: B 1044 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7131 (mt-10)
REVERT: B 1054 ASN cc_start: 0.8375 (t0) cc_final: 0.8174 (t0)
REVERT: B 1058 THR cc_start: 0.8485 (m) cc_final: 0.8240 (p)
REVERT: B 1060 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7917 (mm-30)
REVERT: B 1072 ASP cc_start: 0.7689 (t0) cc_final: 0.7468 (t0)
REVERT: B 1104 MET cc_start: 0.7703 (mtp) cc_final: 0.7467 (ttm)
REVERT: B 1122 GLU cc_start: 0.7475 (tp30) cc_final: 0.7052 (tp30)
REVERT: B 1134 PHE cc_start: 0.6726 (OUTLIER) cc_final: 0.6109 (p90)
  outliers start: 43
  outliers final: 26
  residues processed: 452
  average time/residue: 0.3013
  time to fit residues: 195.8697
Evaluate side-chains
  452 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 422
  time to evaluate  : 1.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  613 GLN
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  650 ASP
Chi-restraints excluded: chain A residue  848 GLU
Chi-restraints excluded: chain A residue  852 LYS
Chi-restraints excluded: chain A residue  855 ASP
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  900 GLN
Chi-restraints excluded: chain A residue  911 GLU
Chi-restraints excluded: chain A residue  926 GLU
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1062 THR
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1112 TRP
Chi-restraints excluded: chain A residue 1134 PHE
Chi-restraints excluded: chain A residue 1189 VAL
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  606 GLU
Chi-restraints excluded: chain B residue  678 MET
Chi-restraints excluded: chain B residue  775 LEU
Chi-restraints excluded: chain B residue  852 LYS
Chi-restraints excluded: chain B residue  916 LEU
Chi-restraints excluded: chain B residue  926 GLU
Chi-restraints excluded: chain B residue 1061 THR
Chi-restraints excluded: chain B residue 1134 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 131 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 112 optimal weight:    0.8980
   chunk 170 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   chunk 144 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 177 optimal weight:    0.6980
   chunk 111 optimal weight:    1.9990
   chunk 164 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 502 HIS
A 981 HIS
** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 HIS
B 192 ASN
B 502 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.154194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.129850 restraints weight = 21980.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 1.61
r_work: 0.3444 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  16492  Z= 0.136
  Angle     :  0.506   8.637  22364  Z= 0.271
  Chirality :  0.041   0.147   2688
  Planarity :  0.004   0.060   2750
  Dihedral  :  3.979  38.859   2186
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.40 %
    Favored  : 81.99 %
  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:  2.12 (0.19), residues: 2022
  helix:  1.99 (0.13), residues: 1468
  sheet:  0.91 (0.61), residues: 82
  loop : -0.31 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 278 
 HIS   0.005   0.001   HIS B1120 
 PHE   0.025   0.001   PHE B 769 
 TYR   0.015   0.001   TYR B1009 
 ARG   0.009   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04397 ( 1208)
  hydrogen bonds       : angle       4.06344 ( 3534)
  covalent geometry    : bond        0.00306 (16492)
  covalent geometry    : angle       0.50614 (22364)

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

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

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  470 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 424
  time to evaluate  : 1.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 PHE cc_start: 0.8205 (t80) cc_final: 0.7869 (t80)
REVERT: A  205 MET cc_start: 0.7812 (mmm) cc_final: 0.7231 (mmt)
REVERT: A  289 PHE cc_start: 0.8351 (m-10) cc_final: 0.8124 (m-80)
REVERT: A  300 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7652 (mt-10)
REVERT: A  319 LEU cc_start: 0.8827 (mt) cc_final: 0.8559 (mp)
REVERT: A  383 MET cc_start: 0.8273 (tpp) cc_final: 0.7970 (mmm)
REVERT: A  475 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7950 (mm-40)
REVERT: A  499 ARG cc_start: 0.7780 (ttm170) cc_final: 0.7547 (ttm170)
REVERT: A  511 MET cc_start: 0.8148 (tmm) cc_final: 0.7625 (ttp)
REVERT: A  580 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7361 (tp30)
REVERT: A  591 LYS cc_start: 0.8491 (mtmt) cc_final: 0.8230 (mtpp)
REVERT: A  608 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.8005 (tp)
REVERT: A  621 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7419 (mt-10)
REVERT: A  623 ASP cc_start: 0.7539 (t0) cc_final: 0.7281 (t0)
REVERT: A  628 VAL cc_start: 0.8441 (p) cc_final: 0.7621 (p)
REVERT: A  633 LYS cc_start: 0.8427 (mtmm) cc_final: 0.8106 (mtmm)
REVERT: A  640 ILE cc_start: 0.8124 (mt) cc_final: 0.7713 (tt)
REVERT: A  644 LEU cc_start: 0.8258 (mt) cc_final: 0.8008 (mp)
REVERT: A  645 LYS cc_start: 0.8082 (tttm) cc_final: 0.7845 (tttm)
REVERT: A  678 MET cc_start: 0.7137 (mmm) cc_final: 0.6767 (tmm)
REVERT: A  810 MET cc_start: 0.5526 (ptp) cc_final: 0.5130 (ptp)
REVERT: A  828 LYS cc_start: 0.8435 (mttt) cc_final: 0.8092 (mmmm)
REVERT: A  847 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7316 (mm-30)
REVERT: A  877 GLN cc_start: 0.8473 (tt0) cc_final: 0.8052 (tt0)
REVERT: A  938 MET cc_start: 0.8403 (tpp) cc_final: 0.8115 (mtp)
REVERT: A  989 VAL cc_start: 0.8989 (p) cc_final: 0.8643 (m)
REVERT: A 1003 SER cc_start: 0.8686 (t) cc_final: 0.8310 (m)
REVERT: A 1007 LYS cc_start: 0.8547 (tttt) cc_final: 0.8047 (tttp)
REVERT: A 1033 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7249 (mt-10)
REVERT: A 1037 THR cc_start: 0.8378 (t) cc_final: 0.8138 (m)
REVERT: A 1044 GLU cc_start: 0.7557 (mt-10) cc_final: 0.6860 (mt-10)
REVERT: A 1104 MET cc_start: 0.7822 (mtp) cc_final: 0.7496 (ttp)
REVERT: A 1112 TRP cc_start: 0.5298 (OUTLIER) cc_final: 0.4975 (m-10)
REVERT: A 1134 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.6323 (p90)
REVERT: B   96 LYS cc_start: 0.8314 (ttpt) cc_final: 0.8064 (ttpt)
REVERT: B  160 MET cc_start: 0.7850 (mmt) cc_final: 0.7618 (mmm)
REVERT: B  205 MET cc_start: 0.7999 (mmm) cc_final: 0.7794 (mmp)
REVERT: B  233 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7461 (tt0)
REVERT: B  250 LYS cc_start: 0.8601 (mttt) cc_final: 0.8330 (mttp)
REVERT: B  339 THR cc_start: 0.8615 (m) cc_final: 0.8402 (p)
REVERT: B  355 MET cc_start: 0.8433 (tmm) cc_final: 0.7854 (ttp)
REVERT: B  383 MET cc_start: 0.8350 (tpp) cc_final: 0.7900 (mmm)
REVERT: B  387 TYR cc_start: 0.8490 (m-10) cc_final: 0.8134 (m-10)
REVERT: B  580 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7403 (tp30)
REVERT: B  590 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7855 (mt-10)
REVERT: B  610 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8083 (mp)
REVERT: B  621 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7444 (mt-10)
REVERT: B  628 VAL cc_start: 0.8574 (p) cc_final: 0.8185 (p)
REVERT: B  632 LYS cc_start: 0.8471 (ttmm) cc_final: 0.7973 (ttmm)
REVERT: B  633 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8299 (mmtm)
REVERT: B  697 MET cc_start: 0.5834 (ttt) cc_final: 0.5518 (ttt)
REVERT: B  810 MET cc_start: 0.5541 (ptp) cc_final: 0.5015 (ptp)
REVERT: B  847 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7486 (mm-30)
REVERT: B  849 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7704 (mt-10)
REVERT: B  877 GLN cc_start: 0.8535 (tt0) cc_final: 0.8113 (tt0)
REVERT: B  967 MET cc_start: 0.7519 (mmm) cc_final: 0.7271 (mmm)
REVERT: B 1007 LYS cc_start: 0.8584 (tttt) cc_final: 0.8158 (tttp)
REVERT: B 1033 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7344 (mt-10)
REVERT: B 1037 THR cc_start: 0.8327 (t) cc_final: 0.8090 (m)
REVERT: B 1044 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7236 (mt-10)
REVERT: B 1054 ASN cc_start: 0.8355 (t0) cc_final: 0.8135 (t0)
REVERT: B 1058 THR cc_start: 0.8450 (m) cc_final: 0.8244 (p)
REVERT: B 1060 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7896 (mm-30)
REVERT: B 1075 ILE cc_start: 0.8718 (mm) cc_final: 0.8430 (mt)
REVERT: B 1104 MET cc_start: 0.7568 (mtp) cc_final: 0.7294 (ttp)
REVERT: B 1134 PHE cc_start: 0.6721 (OUTLIER) cc_final: 0.6106 (p90)
  outliers start: 46
  outliers final: 28
  residues processed: 447
  average time/residue: 0.3024
  time to fit residues: 194.8745
Evaluate side-chains
  445 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 412
  time to evaluate  : 1.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  613 GLN
Chi-restraints excluded: chain A residue  822 ILE
Chi-restraints excluded: chain A residue  852 LYS
Chi-restraints excluded: chain A residue  855 ASP
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  900 GLN
Chi-restraints excluded: chain A residue  911 GLU
Chi-restraints excluded: chain A residue  926 GLU
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1112 TRP
Chi-restraints excluded: chain A residue 1134 PHE
Chi-restraints excluded: chain A residue 1189 VAL
Chi-restraints excluded: chain A residue 1191 ASN
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  606 GLU
Chi-restraints excluded: chain B residue  610 LEU
Chi-restraints excluded: chain B residue  627 LEU
Chi-restraints excluded: chain B residue  678 MET
Chi-restraints excluded: chain B residue  775 LEU
Chi-restraints excluded: chain B residue  855 ASP
Chi-restraints excluded: chain B residue  916 LEU
Chi-restraints excluded: chain B residue  926 GLU
Chi-restraints excluded: chain B residue  970 ILE
Chi-restraints excluded: chain B residue 1134 PHE
Chi-restraints excluded: chain B residue 1189 VAL
Chi-restraints excluded: chain B residue 1191 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 81 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 93 optimal weight:    1.9990
   chunk 94 optimal weight:    0.5980
   chunk 85 optimal weight:    0.5980
   chunk 179 optimal weight:    0.0470
   chunk 181 optimal weight:    0.9990
   chunk 158 optimal weight:    9.9990
   chunk 130 optimal weight:    0.5980
   chunk 141 optimal weight:    0.7980
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
A 502 HIS
A 981 HIS
** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 HIS
B 502 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.155187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.130971 restraints weight = 22318.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 1.63
r_work: 0.3475 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3317 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  16492  Z= 0.117
  Angle     :  0.495   9.178  22364  Z= 0.262
  Chirality :  0.040   0.142   2688
  Planarity :  0.004   0.067   2750
  Dihedral  :  3.870  38.693   2186
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 15.91 %
    Favored  : 81.70 %
  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:  2.30 (0.19), residues: 2022
  helix:  2.12 (0.13), residues: 1468
  sheet:  1.02 (0.61), residues: 82
  loop : -0.25 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 278 
 HIS   0.004   0.001   HIS B 676 
 PHE   0.026   0.001   PHE B 769 
 TYR   0.013   0.001   TYR B1009 
 ARG   0.008   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04086 ( 1208)
  hydrogen bonds       : angle       3.96224 ( 3534)
  covalent geometry    : bond        0.00255 (16492)
  covalent geometry    : angle       0.49472 (22364)

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

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

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  453 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 411
  time to evaluate  : 1.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ASN cc_start: 0.8511 (m-40) cc_final: 0.8184 (m-40)
REVERT: A  289 PHE cc_start: 0.8316 (m-10) cc_final: 0.8085 (m-80)
REVERT: A  300 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7646 (mt-10)
REVERT: A  383 MET cc_start: 0.8288 (tpp) cc_final: 0.8024 (mmm)
REVERT: A  475 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7959 (mm-40)
REVERT: A  499 ARG cc_start: 0.7787 (ttm170) cc_final: 0.7549 (ttm170)
REVERT: A  580 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7575 (tp30)
REVERT: A  591 LYS cc_start: 0.8482 (mtmt) cc_final: 0.8234 (mtpp)
REVERT: A  608 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7996 (tp)
REVERT: A  621 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7444 (mt-10)
REVERT: A  623 ASP cc_start: 0.7512 (t0) cc_final: 0.7310 (t0)
REVERT: A  628 VAL cc_start: 0.8386 (p) cc_final: 0.7518 (p)
REVERT: A  633 LYS cc_start: 0.8416 (mtmm) cc_final: 0.8102 (mtmm)
REVERT: A  640 ILE cc_start: 0.8083 (mt) cc_final: 0.7763 (tt)
REVERT: A  644 LEU cc_start: 0.8264 (mt) cc_final: 0.8045 (mp)
REVERT: A  678 MET cc_start: 0.7096 (mmm) cc_final: 0.6471 (tmm)
REVERT: A  810 MET cc_start: 0.5449 (ptp) cc_final: 0.5067 (ptp)
REVERT: A  828 LYS cc_start: 0.8356 (mttt) cc_final: 0.8027 (mmmm)
REVERT: A  847 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7262 (mm-30)
REVERT: A  877 GLN cc_start: 0.8497 (tt0) cc_final: 0.8074 (tt0)
REVERT: A  938 MET cc_start: 0.8391 (tpp) cc_final: 0.8074 (mtp)
REVERT: A  989 VAL cc_start: 0.8982 (p) cc_final: 0.8633 (m)
REVERT: A 1003 SER cc_start: 0.8711 (t) cc_final: 0.8333 (m)
REVERT: A 1007 LYS cc_start: 0.8549 (tttt) cc_final: 0.8310 (tttp)
REVERT: A 1037 THR cc_start: 0.8354 (t) cc_final: 0.8128 (m)
REVERT: A 1044 GLU cc_start: 0.7592 (mt-10) cc_final: 0.6962 (mt-10)
REVERT: A 1104 MET cc_start: 0.7753 (mtp) cc_final: 0.7477 (ttm)
REVERT: A 1112 TRP cc_start: 0.5228 (OUTLIER) cc_final: 0.4880 (m-10)
REVERT: A 1134 PHE cc_start: 0.6554 (OUTLIER) cc_final: 0.6255 (p90)
REVERT: B   96 LYS cc_start: 0.8308 (ttpt) cc_final: 0.8057 (ttpt)
REVERT: B  160 MET cc_start: 0.7824 (mmt) cc_final: 0.7615 (mmm)
REVERT: B  233 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7424 (tt0)
REVERT: B  250 LYS cc_start: 0.8579 (mttt) cc_final: 0.8298 (mttm)
REVERT: B  355 MET cc_start: 0.8407 (tmm) cc_final: 0.7823 (ttp)
REVERT: B  383 MET cc_start: 0.8328 (tpp) cc_final: 0.7970 (mmm)
REVERT: B  390 ILE cc_start: 0.8666 (mm) cc_final: 0.8449 (mt)
REVERT: B  580 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7416 (tp30)
REVERT: B  610 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8043 (mp)
REVERT: B  621 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7403 (mt-10)
REVERT: B  628 VAL cc_start: 0.8548 (p) cc_final: 0.8151 (p)
REVERT: B  632 LYS cc_start: 0.8452 (ttmm) cc_final: 0.7889 (ttmm)
REVERT: B  633 LYS cc_start: 0.8517 (mtmm) cc_final: 0.8262 (mmtm)
REVERT: B  697 MET cc_start: 0.5843 (ttt) cc_final: 0.5504 (ttt)
REVERT: B  810 MET cc_start: 0.5464 (ptp) cc_final: 0.4989 (ptp)
REVERT: B  847 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7461 (mm-30)
REVERT: B  849 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7702 (mt-10)
REVERT: B  877 GLN cc_start: 0.8551 (tt0) cc_final: 0.8138 (tt0)
REVERT: B  967 MET cc_start: 0.7533 (mmm) cc_final: 0.7232 (mmm)
REVERT: B 1007 LYS cc_start: 0.8617 (tttt) cc_final: 0.8318 (tttm)
REVERT: B 1033 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7683 (mt-10)
REVERT: B 1037 THR cc_start: 0.8314 (t) cc_final: 0.8091 (m)
REVERT: B 1044 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7185 (mt-10)
REVERT: B 1054 ASN cc_start: 0.8334 (t0) cc_final: 0.8118 (t0)
REVERT: B 1060 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7819 (mt-10)
REVERT: B 1075 ILE cc_start: 0.8708 (mm) cc_final: 0.8421 (mt)
REVERT: B 1134 PHE cc_start: 0.6658 (OUTLIER) cc_final: 0.6071 (p90)
  outliers start: 42
  outliers final: 31
  residues processed: 432
  average time/residue: 0.3063
  time to fit residues: 189.8675
Evaluate side-chains
  436 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 400
  time to evaluate  : 1.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  613 GLN
Chi-restraints excluded: chain A residue  822 ILE
Chi-restraints excluded: chain A residue  852 LYS
Chi-restraints excluded: chain A residue  855 ASP
Chi-restraints excluded: chain A residue  900 GLN
Chi-restraints excluded: chain A residue  926 GLU
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1062 THR
Chi-restraints excluded: chain A residue 1112 TRP
Chi-restraints excluded: chain A residue 1134 PHE
Chi-restraints excluded: chain A residue 1146 ILE
Chi-restraints excluded: chain A residue 1189 VAL
Chi-restraints excluded: chain A residue 1191 ASN
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  606 GLU
Chi-restraints excluded: chain B residue  610 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  678 MET
Chi-restraints excluded: chain B residue  775 LEU
Chi-restraints excluded: chain B residue  822 ILE
Chi-restraints excluded: chain B residue  852 LYS
Chi-restraints excluded: chain B residue  876 LEU
Chi-restraints excluded: chain B residue  916 LEU
Chi-restraints excluded: chain B residue  926 GLU
Chi-restraints excluded: chain B residue  970 ILE
Chi-restraints excluded: chain B residue 1134 PHE
Chi-restraints excluded: chain B residue 1189 VAL
Chi-restraints excluded: chain B residue 1191 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 138 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 98 optimal weight:    7.9990
   chunk 186 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9990
   chunk 124 optimal weight:    1.9990
   chunk 125 optimal weight:    0.8980
   chunk 103 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 111 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 981 HIS
** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 HIS
B 502 HIS
B1106 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.154389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.130362 restraints weight = 22103.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 1.61
r_work: 0.3463 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3306 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16492  Z= 0.145
  Angle     :  0.507  10.005  22364  Z= 0.266
  Chirality :  0.041   0.145   2688
  Planarity :  0.004   0.060   2750
  Dihedral  :  3.844  38.708   2186
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.48 %
    Favored  : 80.80 %
  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:  2.26 (0.19), residues: 2022
  helix:  2.09 (0.13), residues: 1468
  sheet:  1.05 (0.61), residues: 82
  loop : -0.28 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 278 
 HIS   0.006   0.001   HIS B1120 
 PHE   0.028   0.001   PHE B 769 
 TYR   0.012   0.001   TYR B1009 
 ARG   0.008   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04238 ( 1208)
  hydrogen bonds       : angle       3.96590 ( 3534)
  covalent geometry    : bond        0.00335 (16492)
  covalent geometry    : angle       0.50742 (22364)

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

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

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  472 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 424
  time to evaluate  : 1.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 MET cc_start: 0.7899 (mmt) cc_final: 0.7437 (mmt)
REVERT: A  289 PHE cc_start: 0.8301 (m-10) cc_final: 0.8061 (m-80)
REVERT: A  383 MET cc_start: 0.8320 (tpp) cc_final: 0.8066 (mmm)
REVERT: A  499 ARG cc_start: 0.7775 (ttm170) cc_final: 0.7546 (ttm170)
REVERT: A  511 MET cc_start: 0.8153 (tmm) cc_final: 0.7632 (ttp)
REVERT: A  516 ARG cc_start: 0.8125 (ptm-80) cc_final: 0.7859 (ptm160)
REVERT: A  580 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7553 (tp30)
REVERT: A  590 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7779 (mt-10)
REVERT: A  591 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8242 (mtpp)
REVERT: A  608 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8016 (tp)
REVERT: A  621 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7392 (mt-10)
REVERT: A  623 ASP cc_start: 0.7588 (t0) cc_final: 0.7373 (t0)
REVERT: A  628 VAL cc_start: 0.8373 (p) cc_final: 0.7478 (p)
REVERT: A  633 LYS cc_start: 0.8428 (mtmm) cc_final: 0.8128 (mtmm)
REVERT: A  640 ILE cc_start: 0.8086 (mt) cc_final: 0.7787 (tt)
REVERT: A  644 LEU cc_start: 0.8261 (mt) cc_final: 0.8051 (mp)
REVERT: A  678 MET cc_start: 0.7015 (mmm) cc_final: 0.6361 (tmm)
REVERT: A  810 MET cc_start: 0.5410 (ptp) cc_final: 0.5018 (ptp)
REVERT: A  828 LYS cc_start: 0.8398 (mttt) cc_final: 0.8078 (mmmm)
REVERT: A  847 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7264 (mm-30)
REVERT: A  877 GLN cc_start: 0.8527 (tt0) cc_final: 0.8086 (tt0)
REVERT: A 1003 SER cc_start: 0.8693 (t) cc_final: 0.8344 (m)
REVERT: A 1007 LYS cc_start: 0.8553 (tttt) cc_final: 0.8313 (tttp)
REVERT: A 1037 THR cc_start: 0.8360 (t) cc_final: 0.8125 (m)
REVERT: A 1044 GLU cc_start: 0.7579 (mt-10) cc_final: 0.6984 (mt-10)
REVERT: A 1072 ASP cc_start: 0.7685 (t0) cc_final: 0.7304 (t0)
REVERT: A 1104 MET cc_start: 0.7824 (mtp) cc_final: 0.7557 (ttp)
REVERT: A 1112 TRP cc_start: 0.5298 (OUTLIER) cc_final: 0.4967 (m-10)
REVERT: A 1134 PHE cc_start: 0.6535 (OUTLIER) cc_final: 0.6233 (p90)
REVERT: B   96 LYS cc_start: 0.8333 (ttpt) cc_final: 0.8071 (ttpt)
REVERT: B  160 MET cc_start: 0.7851 (mmt) cc_final: 0.7639 (mmm)
REVERT: B  214 VAL cc_start: 0.8580 (p) cc_final: 0.8363 (m)
REVERT: B  233 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7456 (tt0)
REVERT: B  250 LYS cc_start: 0.8584 (mttt) cc_final: 0.8303 (mttm)
REVERT: B  300 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7592 (mt-10)
REVERT: B  322 SER cc_start: 0.8218 (t) cc_final: 0.7665 (p)
REVERT: B  355 MET cc_start: 0.8423 (tmm) cc_final: 0.7836 (ttp)
REVERT: B  383 MET cc_start: 0.8344 (tpp) cc_final: 0.7988 (mmm)
REVERT: B  390 ILE cc_start: 0.8662 (mm) cc_final: 0.8453 (mt)
REVERT: B  580 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7376 (tp30)
REVERT: B  610 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8149 (mp)
REVERT: B  621 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7454 (mt-10)
REVERT: B  628 VAL cc_start: 0.8540 (p) cc_final: 0.8095 (p)
REVERT: B  632 LYS cc_start: 0.8418 (ttmm) cc_final: 0.7890 (ttmm)
REVERT: B  633 LYS cc_start: 0.8541 (mtmm) cc_final: 0.8268 (mmtm)
REVERT: B  697 MET cc_start: 0.5828 (ttt) cc_final: 0.5576 (ttt)
REVERT: B  847 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7462 (mm-30)
REVERT: B  877 GLN cc_start: 0.8550 (tt0) cc_final: 0.8135 (tt0)
REVERT: B  999 PHE cc_start: 0.7868 (m-80) cc_final: 0.7544 (m-80)
REVERT: B 1007 LYS cc_start: 0.8667 (tttt) cc_final: 0.8290 (tttm)
REVERT: B 1033 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7683 (mt-10)
REVERT: B 1037 THR cc_start: 0.8334 (t) cc_final: 0.8103 (m)
REVERT: B 1044 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7323 (mt-10)
REVERT: B 1060 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7809 (mt-10)
REVERT: B 1123 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8208 (ttp80)
REVERT: B 1134 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.6056 (p90)
REVERT: B 1139 ASP cc_start: 0.7905 (m-30) cc_final: 0.7032 (m-30)
  outliers start: 48
  outliers final: 33
  residues processed: 446
  average time/residue: 0.2957
  time to fit residues: 190.5644
Evaluate side-chains
  457 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 419
  time to evaluate  : 1.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  613 GLN
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  822 ILE
Chi-restraints excluded: chain A residue  852 LYS
Chi-restraints excluded: chain A residue  900 GLN
Chi-restraints excluded: chain A residue  911 GLU
Chi-restraints excluded: chain A residue  926 GLU
Chi-restraints excluded: chain A residue  970 ILE
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1112 TRP
Chi-restraints excluded: chain A residue 1134 PHE
Chi-restraints excluded: chain A residue 1146 ILE
Chi-restraints excluded: chain A residue 1189 VAL
Chi-restraints excluded: chain A residue 1191 ASN
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  606 GLU
Chi-restraints excluded: chain B residue  610 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  678 MET
Chi-restraints excluded: chain B residue  775 LEU
Chi-restraints excluded: chain B residue  822 ILE
Chi-restraints excluded: chain B residue  852 LYS
Chi-restraints excluded: chain B residue  876 LEU
Chi-restraints excluded: chain B residue  916 LEU
Chi-restraints excluded: chain B residue  926 GLU
Chi-restraints excluded: chain B residue  970 ILE
Chi-restraints excluded: chain B residue 1134 PHE
Chi-restraints excluded: chain B residue 1189 VAL
Chi-restraints excluded: chain B residue 1191 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 150 optimal weight:    1.9990
   chunk 120 optimal weight:    0.7980
   chunk 199 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9990
   chunk 196 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0570
   chunk 127 optimal weight:    0.7980
   chunk 165 optimal weight:    5.9990
   chunk 96 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
A 981 HIS
A1114 GLN
** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 HIS
B 502 HIS
B1106 GLN
B1114 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.154852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.130888 restraints weight = 22094.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 1.61
r_work: 0.3456 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  16492  Z= 0.130
  Angle     :  0.510  10.848  22364  Z= 0.266
  Chirality :  0.040   0.140   2688
  Planarity :  0.004   0.065   2750
  Dihedral  :  3.807  38.520   2186
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.27 %
    Favored  : 80.17 %
  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:  2.34 (0.19), residues: 2022
  helix:  2.16 (0.13), residues: 1468
  sheet:  1.17 (0.61), residues: 82
  loop : -0.29 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 278 
 HIS   0.004   0.001   HIS B1120 
 PHE   0.029   0.001   PHE B 769 
 TYR   0.019   0.001   TYR B 313 
 ARG   0.008   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04096 ( 1208)
  hydrogen bonds       : angle       3.91949 ( 3534)
  covalent geometry    : bond        0.00294 (16492)
  covalent geometry    : angle       0.50964 (22364)

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

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

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  475 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 430
  time to evaluate  : 1.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 MET cc_start: 0.7911 (mmt) cc_final: 0.7542 (mmm)
REVERT: A  289 PHE cc_start: 0.8306 (m-10) cc_final: 0.8059 (m-80)
REVERT: A  383 MET cc_start: 0.8314 (tpp) cc_final: 0.8048 (mmm)
REVERT: A  499 ARG cc_start: 0.7740 (ttm170) cc_final: 0.7518 (ttm170)
REVERT: A  511 MET cc_start: 0.8144 (tmm) cc_final: 0.7631 (ttp)
REVERT: A  516 ARG cc_start: 0.8122 (ptm-80) cc_final: 0.7888 (ptm160)
REVERT: A  580 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7535 (tp30)
REVERT: A  591 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8221 (mtpp)
REVERT: A  608 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7999 (tp)
REVERT: A  621 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7388 (mt-10)
REVERT: A  628 VAL cc_start: 0.8320 (p) cc_final: 0.7398 (p)
REVERT: A  633 LYS cc_start: 0.8443 (mtmm) cc_final: 0.8139 (mtmm)
REVERT: A  640 ILE cc_start: 0.8051 (mt) cc_final: 0.7780 (tt)
REVERT: A  644 LEU cc_start: 0.8220 (mt) cc_final: 0.8005 (mp)
REVERT: A  645 LYS cc_start: 0.8057 (tttm) cc_final: 0.7791 (tttp)
REVERT: A  678 MET cc_start: 0.6988 (mmm) cc_final: 0.6295 (tmm)
REVERT: A  810 MET cc_start: 0.5354 (ptp) cc_final: 0.4833 (ptp)
REVERT: A  828 LYS cc_start: 0.8355 (mttt) cc_final: 0.8016 (mmmm)
REVERT: A  847 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7168 (mm-30)
REVERT: A  877 GLN cc_start: 0.8531 (tt0) cc_final: 0.8078 (tt0)
REVERT: A  989 VAL cc_start: 0.8991 (p) cc_final: 0.8624 (m)
REVERT: A 1003 SER cc_start: 0.8724 (t) cc_final: 0.8324 (m)
REVERT: A 1007 LYS cc_start: 0.8569 (tttt) cc_final: 0.8326 (tttp)
REVERT: A 1037 THR cc_start: 0.8356 (t) cc_final: 0.8108 (m)
REVERT: A 1044 GLU cc_start: 0.7583 (mt-10) cc_final: 0.6875 (mt-10)
REVERT: A 1072 ASP cc_start: 0.7719 (t0) cc_final: 0.7317 (t0)
REVERT: A 1104 MET cc_start: 0.7746 (mtp) cc_final: 0.7497 (ttp)
REVERT: A 1112 TRP cc_start: 0.5193 (OUTLIER) cc_final: 0.4845 (m-10)
REVERT: A 1134 PHE cc_start: 0.6516 (OUTLIER) cc_final: 0.6206 (p90)
REVERT: A 1169 ARG cc_start: 0.6618 (mtt180) cc_final: 0.6361 (mtt180)
REVERT: B   96 LYS cc_start: 0.8301 (ttpt) cc_final: 0.8020 (ttpt)
REVERT: B  160 MET cc_start: 0.7840 (mmt) cc_final: 0.7618 (mmm)
REVERT: B  214 VAL cc_start: 0.8549 (p) cc_final: 0.8343 (m)
REVERT: B  233 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7440 (tt0)
REVERT: B  250 LYS cc_start: 0.8552 (mttt) cc_final: 0.8288 (mttp)
REVERT: B  300 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7613 (mt-10)
REVERT: B  322 SER cc_start: 0.8206 (t) cc_final: 0.7658 (p)
REVERT: B  355 MET cc_start: 0.8417 (tmm) cc_final: 0.7847 (ttp)
REVERT: B  383 MET cc_start: 0.8322 (tpp) cc_final: 0.7957 (mmm)
REVERT: B  390 ILE cc_start: 0.8653 (mm) cc_final: 0.8443 (mt)
REVERT: B  580 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7363 (tp30)
REVERT: B  610 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8094 (mp)
REVERT: B  621 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7450 (mt-10)
REVERT: B  632 LYS cc_start: 0.8422 (ttmm) cc_final: 0.8192 (ttmt)
REVERT: B  633 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8267 (mmtm)
REVERT: B  697 MET cc_start: 0.5907 (ttt) cc_final: 0.5627 (ttt)
REVERT: B  810 MET cc_start: 0.5397 (ptp) cc_final: 0.5193 (ptp)
REVERT: B  847 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7495 (mm-30)
REVERT: B  877 GLN cc_start: 0.8570 (tt0) cc_final: 0.8191 (tt0)
REVERT: B  881 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7711 (mt-10)
REVERT: B  915 GLU cc_start: 0.7785 (tt0) cc_final: 0.7584 (tp30)
REVERT: B  987 VAL cc_start: 0.8880 (t) cc_final: 0.8591 (m)
REVERT: B 1007 LYS cc_start: 0.8637 (tttt) cc_final: 0.8390 (tttm)
REVERT: B 1037 THR cc_start: 0.8370 (t) cc_final: 0.8113 (m)
REVERT: B 1044 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7279 (mt-10)
REVERT: B 1060 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7805 (mt-10)
REVERT: B 1075 ILE cc_start: 0.8615 (mm) cc_final: 0.8329 (mt)
REVERT: B 1134 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.6053 (p90)
REVERT: B 1139 ASP cc_start: 0.7896 (m-30) cc_final: 0.6829 (m-30)
  outliers start: 45
  outliers final: 36
  residues processed: 448
  average time/residue: 0.2937
  time to fit residues: 189.4843
Evaluate side-chains
  459 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 418
  time to evaluate  : 1.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  613 GLN
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  822 ILE
Chi-restraints excluded: chain A residue  852 LYS
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  900 GLN
Chi-restraints excluded: chain A residue  926 GLU
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  970 ILE
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1054 ASN
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1112 TRP
Chi-restraints excluded: chain A residue 1134 PHE
Chi-restraints excluded: chain A residue 1146 ILE
Chi-restraints excluded: chain A residue 1189 VAL
Chi-restraints excluded: chain A residue 1191 ASN
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  296 ASP
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  606 GLU
Chi-restraints excluded: chain B residue  610 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  678 MET
Chi-restraints excluded: chain B residue  775 LEU
Chi-restraints excluded: chain B residue  822 ILE
Chi-restraints excluded: chain B residue  852 LYS
Chi-restraints excluded: chain B residue  855 ASP
Chi-restraints excluded: chain B residue  876 LEU
Chi-restraints excluded: chain B residue  916 LEU
Chi-restraints excluded: chain B residue  926 GLU
Chi-restraints excluded: chain B residue  970 ILE
Chi-restraints excluded: chain B residue 1134 PHE
Chi-restraints excluded: chain B residue 1189 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 78 optimal weight:    0.5980
   chunk 121 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 190 optimal weight:    2.9990
   chunk 142 optimal weight:    0.6980
   chunk 137 optimal weight:    0.8980
   chunk 149 optimal weight:    5.9990
   chunk 202 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0370
   chunk 110 optimal weight:    0.0770
   chunk 152 optimal weight:    3.9990
   overall best weight:    0.4616

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

Flipped N/Q/H residues before XYZ refinement:
A 502 HIS
A 981 HIS
** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 HIS
B 502 HIS
B 981 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.155561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.131501 restraints weight = 22009.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 1.62
r_work: 0.3474 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16492  Z= 0.116
  Angle     :  0.500  11.730  22364  Z= 0.262
  Chirality :  0.040   0.138   2688
  Planarity :  0.004   0.064   2750
  Dihedral  :  3.774  37.978   2186
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 17.50 %
    Favored  : 79.83 %
  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:  2.50 (0.19), residues: 2022
  helix:  2.24 (0.13), residues: 1466
  sheet:  1.32 (0.60), residues: 82
  loop : -0.12 (0.30), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 278 
 HIS   0.004   0.001   HIS B 676 
 PHE   0.030   0.001   PHE B 769 
 TYR   0.012   0.001   TYR B1009 
 ARG   0.010   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03923 ( 1208)
  hydrogen bonds       : angle       3.87558 ( 3534)
  covalent geometry    : bond        0.00252 (16492)
  covalent geometry    : angle       0.50013 (22364)

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

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

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  472 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 425
  time to evaluate  : 1.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 MET cc_start: 0.7918 (mmt) cc_final: 0.7613 (mmm)
REVERT: A  289 PHE cc_start: 0.8296 (m-10) cc_final: 0.8095 (m-80)
REVERT: A  383 MET cc_start: 0.8289 (tpp) cc_final: 0.8042 (mmm)
REVERT: A  451 ILE cc_start: 0.8065 (mm) cc_final: 0.7826 (tp)
REVERT: A  499 ARG cc_start: 0.7752 (ttm170) cc_final: 0.7535 (ttm170)
REVERT: A  511 MET cc_start: 0.8140 (tmm) cc_final: 0.7636 (ttp)
REVERT: A  580 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7507 (tp30)
REVERT: A  591 LYS cc_start: 0.8450 (mtmt) cc_final: 0.8208 (mtpp)
REVERT: A  608 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7979 (tp)
REVERT: A  621 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7407 (mt-10)
REVERT: A  633 LYS cc_start: 0.8437 (mtmm) cc_final: 0.8135 (mtmm)
REVERT: A  640 ILE cc_start: 0.8020 (mt) cc_final: 0.7787 (tt)
REVERT: A  678 MET cc_start: 0.6847 (mmm) cc_final: 0.6575 (tmm)
REVERT: A  810 MET cc_start: 0.5318 (ptp) cc_final: 0.4787 (ptp)
REVERT: A  828 LYS cc_start: 0.8354 (mttt) cc_final: 0.8022 (mmmm)
REVERT: A  847 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7261 (mm-30)
REVERT: A  857 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7594 (tmm)
REVERT: A  877 GLN cc_start: 0.8489 (tt0) cc_final: 0.8102 (tt0)
REVERT: A  989 VAL cc_start: 0.8975 (p) cc_final: 0.8624 (m)
REVERT: A 1003 SER cc_start: 0.8711 (t) cc_final: 0.8322 (m)
REVERT: A 1007 LYS cc_start: 0.8557 (tttt) cc_final: 0.8314 (tttp)
REVERT: A 1037 THR cc_start: 0.8331 (t) cc_final: 0.8079 (m)
REVERT: A 1044 GLU cc_start: 0.7575 (mt-10) cc_final: 0.6945 (mt-10)
REVERT: A 1060 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7749 (mt-10)
REVERT: A 1072 ASP cc_start: 0.7703 (t0) cc_final: 0.7339 (t0)
REVERT: A 1104 MET cc_start: 0.7626 (mtp) cc_final: 0.7409 (ttp)
REVERT: A 1112 TRP cc_start: 0.5155 (OUTLIER) cc_final: 0.4826 (m-10)
REVERT: A 1134 PHE cc_start: 0.6517 (OUTLIER) cc_final: 0.6209 (p90)
REVERT: A 1169 ARG cc_start: 0.6598 (mtt180) cc_final: 0.6344 (mtt180)
REVERT: B   96 LYS cc_start: 0.8286 (ttpt) cc_final: 0.8012 (ttpt)
REVERT: B  160 MET cc_start: 0.7826 (mmt) cc_final: 0.7601 (mmm)
REVERT: B  197 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7459 (mt-10)
REVERT: B  214 VAL cc_start: 0.8537 (p) cc_final: 0.8327 (m)
REVERT: B  233 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7415 (tt0)
REVERT: B  250 LYS cc_start: 0.8540 (mttt) cc_final: 0.8268 (mttp)
REVERT: B  300 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7628 (mt-10)
REVERT: B  322 SER cc_start: 0.8200 (t) cc_final: 0.7665 (p)
REVERT: B  355 MET cc_start: 0.8403 (tmm) cc_final: 0.7828 (ttp)
REVERT: B  383 MET cc_start: 0.8281 (tpp) cc_final: 0.7938 (mmm)
REVERT: B  390 ILE cc_start: 0.8649 (mm) cc_final: 0.8440 (mt)
REVERT: B  580 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7381 (tp30)
REVERT: B  610 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8093 (mp)
REVERT: B  621 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7448 (mt-10)
REVERT: B  633 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8253 (mmtm)
REVERT: B  678 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.5911 (mmm)
REVERT: B  697 MET cc_start: 0.5922 (ttt) cc_final: 0.5645 (ttt)
REVERT: B  810 MET cc_start: 0.5424 (ptp) cc_final: 0.4990 (ptt)
REVERT: B  847 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7466 (mm-30)
REVERT: B  877 GLN cc_start: 0.8529 (tt0) cc_final: 0.8182 (tt0)
REVERT: B  881 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7695 (mt-10)
REVERT: B  987 VAL cc_start: 0.8863 (t) cc_final: 0.8586 (m)
REVERT: B 1007 LYS cc_start: 0.8607 (tttt) cc_final: 0.8363 (tttm)
REVERT: B 1037 THR cc_start: 0.8365 (t) cc_final: 0.8101 (m)
REVERT: B 1044 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7233 (mt-10)
REVERT: B 1060 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7769 (mm-30)
REVERT: B 1075 ILE cc_start: 0.8601 (mm) cc_final: 0.8322 (mt)
REVERT: B 1104 MET cc_start: 0.7708 (mmm) cc_final: 0.7404 (mmm)
REVERT: B 1134 PHE cc_start: 0.6582 (OUTLIER) cc_final: 0.6020 (p90)
REVERT: B 1139 ASP cc_start: 0.7875 (m-30) cc_final: 0.6767 (m-30)
  outliers start: 47
  outliers final: 37
  residues processed: 444
  average time/residue: 0.3014
  time to fit residues: 194.0159
Evaluate side-chains
  464 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 419
  time to evaluate  : 1.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  613 GLN
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  848 GLU
Chi-restraints excluded: chain A residue  852 LYS
Chi-restraints excluded: chain A residue  857 MET
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  900 GLN
Chi-restraints excluded: chain A residue  926 GLU
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  970 ILE
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1054 ASN
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1112 TRP
Chi-restraints excluded: chain A residue 1134 PHE
Chi-restraints excluded: chain A residue 1146 ILE
Chi-restraints excluded: chain A residue 1189 VAL
Chi-restraints excluded: chain A residue 1191 ASN
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  606 GLU
Chi-restraints excluded: chain B residue  610 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  678 MET
Chi-restraints excluded: chain B residue  775 LEU
Chi-restraints excluded: chain B residue  822 ILE
Chi-restraints excluded: chain B residue  852 LYS
Chi-restraints excluded: chain B residue  855 ASP
Chi-restraints excluded: chain B residue  876 LEU
Chi-restraints excluded: chain B residue  916 LEU
Chi-restraints excluded: chain B residue  925 MET
Chi-restraints excluded: chain B residue  926 GLU
Chi-restraints excluded: chain B residue  970 ILE
Chi-restraints excluded: chain B residue 1054 ASN
Chi-restraints excluded: chain B residue 1134 PHE
Chi-restraints excluded: chain B residue 1189 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0070
   chunk 57 optimal weight:    6.9990
   chunk 115 optimal weight:    0.0980
   chunk 140 optimal weight:    0.2980
   chunk 145 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 190 optimal weight:    0.4980
   chunk 112 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9980
   overall best weight:    0.2998

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

Flipped N/Q/H residues before XYZ refinement:
A 502 HIS
A 981 HIS
** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 HIS
B 448 ASN
B 502 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.155668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.131021 restraints weight = 22330.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 1.71
r_work: 0.3464 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  16492  Z= 0.109
  Angle     :  0.505  11.862  22364  Z= 0.263
  Chirality :  0.040   0.297   2688
  Planarity :  0.004   0.064   2750
  Dihedral  :  3.730  37.431   2186
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.18 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.60 (0.19), residues: 2022
  helix:  2.35 (0.13), residues: 1454
  sheet:  1.23 (0.58), residues: 82
  loop : -0.13 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 419 
 HIS   0.004   0.001   HIS A 676 
 PHE   0.030   0.001   PHE B 769 
 TYR   0.011   0.001   TYR B1009 
 ARG   0.011   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03771 ( 1208)
  hydrogen bonds       : angle       3.83255 ( 3534)
  covalent geometry    : bond        0.00228 (16492)
  covalent geometry    : angle       0.50523 (22364)

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

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

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  466 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 424
  time to evaluate  : 1.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ASN cc_start: 0.8473 (m-40) cc_final: 0.8146 (m-40)
REVERT: A  205 MET cc_start: 0.7938 (mmt) cc_final: 0.7601 (mmm)
REVERT: A  289 PHE cc_start: 0.8302 (m-10) cc_final: 0.8076 (m-80)
REVERT: A  300 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7591 (mt-10)
REVERT: A  383 MET cc_start: 0.8287 (tpp) cc_final: 0.8019 (mmm)
REVERT: A  451 ILE cc_start: 0.8083 (mm) cc_final: 0.7836 (tp)
REVERT: A  499 ARG cc_start: 0.7658 (ttm170) cc_final: 0.7438 (ttm170)
REVERT: A  511 MET cc_start: 0.8164 (tmm) cc_final: 0.7689 (ttp)
REVERT: A  580 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7509 (tp30)
REVERT: A  591 LYS cc_start: 0.8454 (mtmt) cc_final: 0.8184 (mtpp)
REVERT: A  608 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7928 (tp)
REVERT: A  621 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7415 (mt-10)
REVERT: A  633 LYS cc_start: 0.8412 (mtmm) cc_final: 0.8092 (mtmm)
REVERT: A  678 MET cc_start: 0.6803 (mmm) cc_final: 0.6543 (tmm)
REVERT: A  810 MET cc_start: 0.5337 (ptp) cc_final: 0.4790 (ptp)
REVERT: A  828 LYS cc_start: 0.8325 (mttt) cc_final: 0.7969 (mmmm)
REVERT: A  847 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7303 (mm-30)
REVERT: A  857 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7614 (tmm)
REVERT: A  877 GLN cc_start: 0.8556 (tt0) cc_final: 0.8225 (tt0)
REVERT: A  989 VAL cc_start: 0.8935 (p) cc_final: 0.8621 (m)
REVERT: A 1003 SER cc_start: 0.8740 (t) cc_final: 0.8345 (m)
REVERT: A 1007 LYS cc_start: 0.8559 (tttt) cc_final: 0.7967 (tttp)
REVERT: A 1033 GLU cc_start: 0.7587 (mt-10) cc_final: 0.6924 (mt-10)
REVERT: A 1037 THR cc_start: 0.8370 (t) cc_final: 0.8086 (m)
REVERT: A 1044 GLU cc_start: 0.7580 (mt-10) cc_final: 0.6952 (mt-10)
REVERT: A 1060 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7670 (mt-10)
REVERT: A 1072 ASP cc_start: 0.7717 (t0) cc_final: 0.7341 (t0)
REVERT: A 1104 MET cc_start: 0.7593 (mtp) cc_final: 0.7350 (ttp)
REVERT: A 1112 TRP cc_start: 0.5169 (OUTLIER) cc_final: 0.4882 (m-10)
REVERT: A 1134 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.6234 (p90)
REVERT: A 1169 ARG cc_start: 0.6531 (mtt180) cc_final: 0.6263 (mtt180)
REVERT: B   96 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7972 (ttpt)
REVERT: B  160 MET cc_start: 0.7863 (mmt) cc_final: 0.7622 (mmm)
REVERT: B  197 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7501 (mt-10)
REVERT: B  214 VAL cc_start: 0.8527 (p) cc_final: 0.8320 (m)
REVERT: B  233 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7408 (tt0)
REVERT: B  250 LYS cc_start: 0.8501 (mttt) cc_final: 0.8187 (mttm)
REVERT: B  300 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7617 (mt-10)
REVERT: B  322 SER cc_start: 0.8210 (t) cc_final: 0.7666 (p)
REVERT: B  355 MET cc_start: 0.8364 (tmm) cc_final: 0.7795 (ttp)
REVERT: B  383 MET cc_start: 0.8297 (tpp) cc_final: 0.7929 (mmm)
REVERT: B  390 ILE cc_start: 0.8604 (mm) cc_final: 0.8380 (mt)
REVERT: B  580 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7165 (tp30)
REVERT: B  610 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8038 (mp)
REVERT: B  621 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7421 (mt-10)
REVERT: B  632 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8196 (ttmm)
REVERT: B  633 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8195 (mmtm)
REVERT: B  678 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.5993 (mmm)
REVERT: B  697 MET cc_start: 0.5883 (ttt) cc_final: 0.5602 (ttt)
REVERT: B  810 MET cc_start: 0.5421 (ptp) cc_final: 0.5211 (ptp)
REVERT: B  847 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7540 (mm-30)
REVERT: B  877 GLN cc_start: 0.8575 (tt0) cc_final: 0.8238 (tt0)
REVERT: B  987 VAL cc_start: 0.8905 (t) cc_final: 0.8629 (m)
REVERT: B 1007 LYS cc_start: 0.8601 (tttt) cc_final: 0.8182 (tttm)
REVERT: B 1033 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7505 (mt-10)
REVERT: B 1037 THR cc_start: 0.8406 (t) cc_final: 0.8080 (m)
REVERT: B 1044 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7126 (mt-10)
REVERT: B 1075 ILE cc_start: 0.8564 (mm) cc_final: 0.8268 (mt)
REVERT: B 1104 MET cc_start: 0.7714 (mmm) cc_final: 0.7418 (mmm)
REVERT: B 1134 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.6070 (p90)
REVERT: B 1139 ASP cc_start: 0.7870 (m-30) cc_final: 0.6786 (m-30)
  outliers start: 42
  outliers final: 31
  residues processed: 446
  average time/residue: 0.2930
  time to fit residues: 190.3021
Evaluate side-chains
  451 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 413
  time to evaluate  : 1.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  613 GLN
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  852 LYS
Chi-restraints excluded: chain A residue  857 MET
Chi-restraints excluded: chain A residue  900 GLN
Chi-restraints excluded: chain A residue  926 GLU
Chi-restraints excluded: chain A residue  970 ILE
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1054 ASN
Chi-restraints excluded: chain A residue 1112 TRP
Chi-restraints excluded: chain A residue 1134 PHE
Chi-restraints excluded: chain A residue 1146 ILE
Chi-restraints excluded: chain A residue 1189 VAL
Chi-restraints excluded: chain A residue 1191 ASN
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  606 GLU
Chi-restraints excluded: chain B residue  610 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  678 MET
Chi-restraints excluded: chain B residue  775 LEU
Chi-restraints excluded: chain B residue  822 ILE
Chi-restraints excluded: chain B residue  852 LYS
Chi-restraints excluded: chain B residue  876 LEU
Chi-restraints excluded: chain B residue  916 LEU
Chi-restraints excluded: chain B residue  925 MET
Chi-restraints excluded: chain B residue  926 GLU
Chi-restraints excluded: chain B residue  970 ILE
Chi-restraints excluded: chain B residue 1054 ASN
Chi-restraints excluded: chain B residue 1134 PHE
Chi-restraints excluded: chain B residue 1189 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 148 optimal weight:    0.9990
   chunk 128 optimal weight:    0.4980
   chunk 47 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   chunk 181 optimal weight:    2.9990
   chunk 143 optimal weight:    0.0470
   chunk 126 optimal weight:    0.6980
   chunk 151 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
A 502 HIS
A 981 HIS
** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 502 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.154938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.130340 restraints weight = 22296.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 1.69
r_work: 0.3455 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  16492  Z= 0.123
  Angle     :  0.525  12.165  22364  Z= 0.269
  Chirality :  0.040   0.257   2688
  Planarity :  0.004   0.066   2750
  Dihedral  :  3.728  37.334   2186
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.58 %
    Favored  : 79.03 %
  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:  2.56 (0.19), residues: 2022
  helix:  2.30 (0.13), residues: 1462
  sheet:  1.27 (0.58), residues: 82
  loop : -0.12 (0.30), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 643 
 HIS   0.004   0.001   HIS B 676 
 PHE   0.031   0.001   PHE B 769 
 TYR   0.012   0.001   TYR B1009 
 ARG   0.010   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03923 ( 1208)
  hydrogen bonds       : angle       3.86204 ( 3534)
  covalent geometry    : bond        0.00274 (16492)
  covalent geometry    : angle       0.52523 (22364)

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

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

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4044 Ramachandran restraints generated.
    2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  455 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 413
  time to evaluate  : 1.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ASN cc_start: 0.8462 (m-40) cc_final: 0.8156 (m-40)
REVERT: A  205 MET cc_start: 0.7947 (mmt) cc_final: 0.7596 (mmm)
REVERT: A  289 PHE cc_start: 0.8315 (m-10) cc_final: 0.8093 (m-80)
REVERT: A  383 MET cc_start: 0.8278 (tpp) cc_final: 0.8003 (mmm)
REVERT: A  451 ILE cc_start: 0.8087 (mm) cc_final: 0.7852 (tp)
REVERT: A  499 ARG cc_start: 0.7731 (ttm170) cc_final: 0.7523 (ttm170)
REVERT: A  511 MET cc_start: 0.8181 (tmm) cc_final: 0.7695 (ttp)
REVERT: A  580 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7435 (tp30)
REVERT: A  591 LYS cc_start: 0.8451 (mtmt) cc_final: 0.8192 (mtpp)
REVERT: A  608 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7964 (tp)
REVERT: A  621 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7464 (mt-10)
REVERT: A  633 LYS cc_start: 0.8421 (mtmm) cc_final: 0.8113 (mtmm)
REVERT: A  678 MET cc_start: 0.6749 (mmm) cc_final: 0.6517 (tmm)
REVERT: A  810 MET cc_start: 0.5353 (ptp) cc_final: 0.4806 (ptp)
REVERT: A  828 LYS cc_start: 0.8343 (mttt) cc_final: 0.8008 (mmmm)
REVERT: A  847 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7316 (mm-30)
REVERT: A  877 GLN cc_start: 0.8572 (tt0) cc_final: 0.8231 (tt0)
REVERT: A  989 VAL cc_start: 0.8950 (p) cc_final: 0.8633 (m)
REVERT: A 1003 SER cc_start: 0.8715 (t) cc_final: 0.8322 (m)
REVERT: A 1007 LYS cc_start: 0.8601 (tttt) cc_final: 0.8011 (tttp)
REVERT: A 1033 GLU cc_start: 0.7602 (mt-10) cc_final: 0.6999 (mt-10)
REVERT: A 1037 THR cc_start: 0.8366 (t) cc_final: 0.8074 (m)
REVERT: A 1044 GLU cc_start: 0.7596 (mt-10) cc_final: 0.6948 (mt-10)
REVERT: A 1060 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7705 (mt-10)
REVERT: A 1072 ASP cc_start: 0.7716 (t0) cc_final: 0.7350 (t0)
REVERT: A 1104 MET cc_start: 0.7572 (mtp) cc_final: 0.7346 (ttp)
REVERT: A 1112 TRP cc_start: 0.5193 (OUTLIER) cc_final: 0.4842 (m-10)
REVERT: A 1134 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.6224 (p90)
REVERT: A 1169 ARG cc_start: 0.6542 (mtt180) cc_final: 0.6292 (mtt180)
REVERT: B   96 LYS cc_start: 0.8259 (ttpt) cc_final: 0.7959 (ttpt)
REVERT: B  160 MET cc_start: 0.7895 (mmt) cc_final: 0.7671 (mmm)
REVERT: B  214 VAL cc_start: 0.8555 (p) cc_final: 0.8346 (t)
REVERT: B  233 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7432 (tt0)
REVERT: B  250 LYS cc_start: 0.8488 (mttt) cc_final: 0.8200 (mttp)
REVERT: B  322 SER cc_start: 0.8240 (t) cc_final: 0.7688 (p)
REVERT: B  355 MET cc_start: 0.8427 (tmm) cc_final: 0.7701 (ttp)
REVERT: B  383 MET cc_start: 0.8306 (tpp) cc_final: 0.7938 (mmm)
REVERT: B  390 ILE cc_start: 0.8598 (mm) cc_final: 0.8386 (mt)
REVERT: B  580 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7349 (tp30)
REVERT: B  590 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7812 (mt-10)
REVERT: B  610 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8080 (mp)
REVERT: B  621 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7496 (mt-10)
REVERT: B  632 LYS cc_start: 0.8451 (ttmt) cc_final: 0.8117 (ttmm)
REVERT: B  633 LYS cc_start: 0.8534 (mtmm) cc_final: 0.8221 (mmtm)
REVERT: B  678 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.5966 (mmm)
REVERT: B  697 MET cc_start: 0.5944 (ttt) cc_final: 0.5665 (ttt)
REVERT: B  810 MET cc_start: 0.5463 (ptp) cc_final: 0.5249 (ptp)
REVERT: B  847 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7487 (mm-30)
REVERT: B  877 GLN cc_start: 0.8575 (tt0) cc_final: 0.8291 (tt0)
REVERT: B  881 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7764 (mt-10)
REVERT: B  971 ASP cc_start: 0.7344 (m-30) cc_final: 0.7061 (m-30)
REVERT: B  987 VAL cc_start: 0.8912 (t) cc_final: 0.8624 (m)
REVERT: B 1007 LYS cc_start: 0.8638 (tttt) cc_final: 0.8182 (tttm)
REVERT: B 1033 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7535 (mt-10)
REVERT: B 1037 THR cc_start: 0.8405 (t) cc_final: 0.8075 (m)
REVERT: B 1044 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7117 (mt-10)
REVERT: B 1075 ILE cc_start: 0.8600 (mm) cc_final: 0.8317 (mt)
REVERT: B 1104 MET cc_start: 0.7721 (mmm) cc_final: 0.7415 (mmm)
REVERT: B 1134 PHE cc_start: 0.6606 (OUTLIER) cc_final: 0.6382 (p90)
  outliers start: 42
  outliers final: 31
  residues processed: 435
  average time/residue: 0.3025
  time to fit residues: 189.4813
Evaluate side-chains
  447 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 409
  time to evaluate  : 1.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  613 GLN
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  852 LYS
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  900 GLN
Chi-restraints excluded: chain A residue  926 GLU
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  970 ILE
Chi-restraints excluded: chain A residue  979 LEU
Chi-restraints excluded: chain A residue 1112 TRP
Chi-restraints excluded: chain A residue 1134 PHE
Chi-restraints excluded: chain A residue 1146 ILE
Chi-restraints excluded: chain A residue 1189 VAL
Chi-restraints excluded: chain A residue 1191 ASN
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  606 GLU
Chi-restraints excluded: chain B residue  610 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  678 MET
Chi-restraints excluded: chain B residue  775 LEU
Chi-restraints excluded: chain B residue  822 ILE
Chi-restraints excluded: chain B residue  852 LYS
Chi-restraints excluded: chain B residue  876 LEU
Chi-restraints excluded: chain B residue  916 LEU
Chi-restraints excluded: chain B residue  926 GLU
Chi-restraints excluded: chain B residue  970 ILE
Chi-restraints excluded: chain B residue 1054 ASN
Chi-restraints excluded: chain B residue 1134 PHE
Chi-restraints excluded: chain B residue 1189 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 138 optimal weight:    1.9990
   chunk 20 optimal weight:    0.3980
   chunk 47 optimal weight:    4.9990
   chunk 156 optimal weight:    4.9990
   chunk 60 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 185 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9980
   chunk 192 optimal weight:    4.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 502 HIS
A 981 HIS
** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 502 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.153329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.128625 restraints weight = 22217.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 1.69
r_work: 0.3431 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.3226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  16492  Z= 0.160
  Angle     :  0.555  11.795  22364  Z= 0.284
  Chirality :  0.042   0.267   2688
  Planarity :  0.004   0.065   2750
  Dihedral  :  3.784  37.246   2186
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 18.92 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.40 (0.19), residues: 2022
  helix:  2.17 (0.13), residues: 1466
  sheet:  1.27 (0.59), residues: 82
  loop : -0.19 (0.30), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1112 
 HIS   0.006   0.001   HIS B1120 
 PHE   0.031   0.001   PHE B 769 
 TYR   0.014   0.001   TYR B1009 
 ARG   0.009   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04258 ( 1208)
  hydrogen bonds       : angle       3.95952 ( 3534)
  covalent geometry    : bond        0.00374 (16492)
  covalent geometry    : angle       0.55536 (22364)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9682.68 seconds
wall clock time: 165 minutes 56.36 seconds (9956.36 seconds total)