Starting phenix.real_space_refine
on Thu May 15 05:57:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cq1_45806/05_2025/9cq1_45806.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cq1_45806/05_2025/9cq1_45806.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cq1_45806/05_2025/9cq1_45806.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cq1_45806/05_2025/9cq1_45806.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cq1_45806/05_2025/9cq1_45806.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cq1_45806/05_2025/9cq1_45806.cif"
  }
  resolution = 4.3
  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=   0.000 sd=   0.005
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     104      5.16       5
     C    8158      2.51       5
     N    2230      2.21       5
     O    2448      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 98 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 12940
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6470
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 847, 6470
          Classifications: {'peptide': 847}
          Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 798}
    Chain: "B"
      Number of atoms: 6470
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 847, 6470
          Classifications: {'peptide': 847}
          Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 798}
  Time building chain proxies: 9.38, per 1000 atoms: 0.72
  Number of scatterers: 12940
  At special positions: 0
  Unit cell: (205.11, 90.1, 84.27, 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     104     16.00
     O    2448      8.00
     N    2230      7.00
     C    8158      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.15
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3136

  Finding SS restraints...
    Secondary structure from input PDB file:
      83 helices and 11 sheets defined
      46.6% alpha, 14.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 53
    Processing helix  chain 'A' and resid 68 through 72
    Processing helix  chain 'A' and resid 93 through 99
      removed outlier: 3.580A  pdb=" N   MET A  99 " --> pdb=" O   LYS A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 118
      removed outlier: 3.535A  pdb=" N   GLU A 109 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 126
    Processing helix  chain 'A' and resid 139 through 146
    Processing helix  chain 'A' and resid 147 through 149
      No H-bonds generated for 'chain 'A' and resid 147 through 149'
    Processing helix  chain 'A' and resid 150 through 151
      No H-bonds generated for 'chain 'A' and resid 150 through 151'
    Processing helix  chain 'A' and resid 152 through 157
    Processing helix  chain 'A' and resid 160 through 171
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 184 through 199
    Processing helix  chain 'A' and resid 215 through 225
      removed outlier: 3.714A  pdb=" N   SER A 219 " --> pdb=" O   ARG A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 260
      No H-bonds generated for 'chain 'A' and resid 258 through 260'
    Processing helix  chain 'A' and resid 286 through 302
    Processing helix  chain 'A' and resid 304 through 306
      No H-bonds generated for 'chain 'A' and resid 304 through 306'
    Processing helix  chain 'A' and resid 320 through 334
    Processing helix  chain 'A' and resid 347 through 352
    Processing helix  chain 'A' and resid 354 through 356
      No H-bonds generated for 'chain 'A' and resid 354 through 356'
    Processing helix  chain 'A' and resid 357 through 373
      removed outlier: 4.102A  pdb=" N   ALA A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 393
    Processing helix  chain 'A' and resid 452 through 466
    Processing helix  chain 'A' and resid 469 through 480
    Processing helix  chain 'A' and resid 531 through 534
    Processing helix  chain 'A' and resid 535 through 550
    Processing helix  chain 'A' and resid 551 through 553
      No H-bonds generated for 'chain 'A' and resid 551 through 553'
    Processing helix  chain 'A' and resid 555 through 563
    Processing helix  chain 'A' and resid 566 through 570
      removed outlier: 3.881A  pdb=" N   THR A 570 " --> pdb=" O   THR A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 592
      removed outlier: 4.280A  pdb=" N   PHE A 575 " --> pdb=" O   ILE A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 613
      removed outlier: 4.113A  pdb=" N   GLY A 608 " --> pdb=" O   MET A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 635
    Processing helix  chain 'A' and resid 648 through 656
    Processing helix  chain 'A' and resid 677 through 690
    Processing helix  chain 'A' and resid 706 through 708
      No H-bonds generated for 'chain 'A' and resid 706 through 708'
    Processing helix  chain 'A' and resid 709 through 722
      removed outlier: 4.434A  pdb=" N   ALA A 714 " --> pdb=" O   GLU A 710 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   SER A 715 " --> pdb=" O   ASN A 711 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LYS A 722 " --> pdb=" O   ASP A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 743
    Processing helix  chain 'A' and resid 752 through 762
      removed outlier: 3.761A  pdb=" N   LEU A 760 " --> pdb=" O   HIS A 756 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   VAL A 761 " --> pdb=" O   ALA A 757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 765 through 771
    Processing helix  chain 'A' and resid 788 through 797
    Processing helix  chain 'A' and resid 812 through 827
    Processing helix  chain 'A' and resid 832 through 837
      removed outlier: 4.039A  pdb=" N   CYS A 836 " --> pdb=" O   PRO A 833 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 851 through 857
    Processing helix  chain 'B' and resid 43 through 53
    Processing helix  chain 'B' and resid 68 through 72
    Processing helix  chain 'B' and resid 93 through 99
      removed outlier: 3.587A  pdb=" N   MET B  99 " --> pdb=" O   LYS B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 118
      removed outlier: 3.532A  pdb=" N   GLU B 109 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 126
    Processing helix  chain 'B' and resid 139 through 146
    Processing helix  chain 'B' and resid 147 through 150
      removed outlier: 6.093A  pdb=" N   ASP B 150 " --> pdb=" O   CYS B 147 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 147 through 150'
    Processing helix  chain 'B' and resid 151 through 157
      removed outlier: 4.142A  pdb=" N   MET B 155 " --> pdb=" O   PRO B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 171
    Processing helix  chain 'B' and resid 181 through 183
      No H-bonds generated for 'chain 'B' and resid 181 through 183'
    Processing helix  chain 'B' and resid 184 through 199
    Processing helix  chain 'B' and resid 215 through 225
      removed outlier: 3.713A  pdb=" N   SER B 219 " --> pdb=" O   ARG B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 260
      No H-bonds generated for 'chain 'B' and resid 258 through 260'
    Processing helix  chain 'B' and resid 286 through 302
    Processing helix  chain 'B' and resid 304 through 306
      No H-bonds generated for 'chain 'B' and resid 304 through 306'
    Processing helix  chain 'B' and resid 320 through 334
    Processing helix  chain 'B' and resid 347 through 352
    Processing helix  chain 'B' and resid 354 through 356
      No H-bonds generated for 'chain 'B' and resid 354 through 356'
    Processing helix  chain 'B' and resid 357 through 373
      removed outlier: 4.086A  pdb=" N   ALA B 361 " --> pdb=" O   GLY B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 393
    Processing helix  chain 'B' and resid 452 through 466
    Processing helix  chain 'B' and resid 469 through 480
    Processing helix  chain 'B' and resid 531 through 534
    Processing helix  chain 'B' and resid 535 through 550
    Processing helix  chain 'B' and resid 551 through 553
      No H-bonds generated for 'chain 'B' and resid 551 through 553'
    Processing helix  chain 'B' and resid 555 through 563
    Processing helix  chain 'B' and resid 566 through 570
      removed outlier: 3.895A  pdb=" N   THR B 570 " --> pdb=" O   THR B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 592
      removed outlier: 4.261A  pdb=" N   PHE B 575 " --> pdb=" O   ILE B 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 604 through 613
      removed outlier: 4.106A  pdb=" N   GLY B 608 " --> pdb=" O   MET B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 617 through 635
    Processing helix  chain 'B' and resid 648 through 656
    Processing helix  chain 'B' and resid 677 through 690
    Processing helix  chain 'B' and resid 706 through 708
      No H-bonds generated for 'chain 'B' and resid 706 through 708'
    Processing helix  chain 'B' and resid 709 through 722
      removed outlier: 4.421A  pdb=" N   ALA B 714 " --> pdb=" O   GLU B 710 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   SER B 715 " --> pdb=" O   ASN B 711 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LYS B 722 " --> pdb=" O   ASP B 718 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 739 through 743
    Processing helix  chain 'B' and resid 752 through 762
      removed outlier: 3.750A  pdb=" N   LEU B 760 " --> pdb=" O   HIS B 756 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   VAL B 761 " --> pdb=" O   ALA B 757 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 765 through 771
    Processing helix  chain 'B' and resid 788 through 797
    Processing helix  chain 'B' and resid 812 through 827
    Processing helix  chain 'B' and resid 832 through 837
      removed outlier: 4.021A  pdb=" N   CYS B 836 " --> pdb=" O   PRO B 833 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 851 through 857
    Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 398
      removed outlier: 7.077A  pdb=" N   TYR A 409 " --> pdb=" O   VAL A 308 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   TYR A 310 " --> pdb=" O   TYR A 409 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   ASN A 421 " --> pdb=" O   THR A 272 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   THR A 272 " --> pdb=" O   ASN A 421 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   HIS A 423 " --> pdb=" O   VAL A 270 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   VAL A 270 " --> pdb=" O   HIS A 423 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   VAL A 425 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   CYS A 265 " --> pdb=" O   ILE A  31 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   ILE A  29 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 5.128A  pdb=" N   ILE A  31 " --> pdb=" O   LYS A 255 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   LYS A 255 " --> pdb=" O   ILE A  31 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   GLY A 131 " --> pdb=" O   ILE A 206 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   ALA A 208 " --> pdb=" O   GLY A 131 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   TYR A 133 " --> pdb=" O   ALA A 208 " (cutoff:3.500A)
      removed outlier: 8.095A  pdb=" N   VAL A 210 " --> pdb=" O   TYR A 133 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ALA A 135 " --> pdb=" O   VAL A 210 " (cutoff:3.500A)
      removed outlier: 8.734A  pdb=" N   ILE A 177 " --> pdb=" O   THR A 130 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   MET A 132 " --> pdb=" O   ILE A 177 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   TYR A 179 " --> pdb=" O   MET A 132 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   LEU A 134 " --> pdb=" O   TYR A 179 " (cutoff:3.500A)
      removed outlier: 8.732A  pdb=" N   ILE B 177 " --> pdb=" O   THR B 130 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   MET B 132 " --> pdb=" O   ILE B 177 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   TYR B 179 " --> pdb=" O   MET B 132 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   LEU B 134 " --> pdb=" O   TYR B 179 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   GLY B 131 " --> pdb=" O   ILE B 206 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   ALA B 208 " --> pdb=" O   GLY B 131 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   TYR B 133 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 8.095A  pdb=" N   VAL B 210 " --> pdb=" O   TYR B 133 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   ALA B 135 " --> pdb=" O   VAL B 210 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   LYS B 255 " --> pdb=" O   ILE B  31 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   ILE B  31 " --> pdb=" O   LYS B 255 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   ILE B  29 " --> pdb=" O   VAL B 267 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   CYS B 265 " --> pdb=" O   ILE B  31 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   VAL B 425 " --> pdb=" O   VAL B 268 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   VAL B 270 " --> pdb=" O   HIS B 423 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   HIS B 423 " --> pdb=" O   VAL B 270 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   THR B 272 " --> pdb=" O   ASN B 421 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   ASN B 421 " --> pdb=" O   THR B 272 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   TYR B 409 " --> pdb=" O   VAL B 308 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   TYR B 310 " --> pdb=" O   TYR B 409 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 374 through 375
    Processing sheet with id=AA3, first strand: chain 'A' and resid 444 through 450
    Processing sheet with id=AA4, first strand: chain 'A' and resid 733 through 734
      removed outlier: 6.604A  pdb=" N   ILE A 599 " --> pdb=" O   LEU A 734 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 660 through 667
      removed outlier: 6.585A  pdb=" N   VAL A 660 " --> pdb=" O   ALA A 676 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   ALA A 676 " --> pdb=" O   VAL A 660 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   SER A 674 " --> pdb=" O   PRO A 662 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   SER A 670 " --> pdb=" O   ASN A 666 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   MET A 642 " --> pdb=" O   VAL A 697 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 727 through 728
      removed outlier: 3.938A  pdb=" N   LYS A 727 " --> pdb=" O   SER A 751 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 374 through 375
    Processing sheet with id=AA8, first strand: chain 'B' and resid 444 through 450
    Processing sheet with id=AA9, first strand: chain 'B' and resid 733 through 734
      removed outlier: 6.631A  pdb=" N   ILE B 599 " --> pdb=" O   LEU B 734 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 660 through 667
      removed outlier: 6.613A  pdb=" N   VAL B 660 " --> pdb=" O   ALA B 676 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   ALA B 676 " --> pdb=" O   VAL B 660 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   SER B 674 " --> pdb=" O   PRO B 662 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   SER B 670 " --> pdb=" O   ASN B 666 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   MET B 642 " --> pdb=" O   VAL B 697 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 727 through 728
      removed outlier: 3.920A  pdb=" N   LYS B 727 " --> pdb=" O   SER B 751 " (cutoff:3.500A)

    602 hydrogen bonds defined for protein.
    1728 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: 4.75

  Time building geometry restraints manager: 3.66 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: 3249
        1.33 -     1.46: 2608
        1.46 -     1.58: 7225
        1.58 -     1.70: 0
        1.70 -     1.83: 160
  Bond restraints: 13242
  Sorted by residual:
  bond pdb=" CZ  ARG A  80 "
       pdb=" NH2 ARG A  80 "
    ideal  model  delta    sigma   weight residual
    1.330  1.261  0.069 1.30e-02 5.92e+03 2.85e+01
  bond pdb=" CZ  ARG B  80 "
       pdb=" NH2 ARG B  80 "
    ideal  model  delta    sigma   weight residual
    1.330  1.270  0.060 1.30e-02 5.92e+03 2.13e+01
  bond pdb=" CZ  ARG A 530 "
       pdb=" NH2 ARG A 530 "
    ideal  model  delta    sigma   weight residual
    1.330  1.283  0.047 1.30e-02 5.92e+03 1.29e+01
  bond pdb=" CZ  ARG A 490 "
       pdb=" NH2 ARG A 490 "
    ideal  model  delta    sigma   weight residual
    1.330  1.283  0.047 1.30e-02 5.92e+03 1.29e+01
  bond pdb=" CZ  ARG B  37 "
       pdb=" NH2 ARG B  37 "
    ideal  model  delta    sigma   weight residual
    1.330  1.284  0.046 1.30e-02 5.92e+03 1.24e+01
  ... (remaining 13237 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 12345
        1.42 -     2.84: 4399
        2.84 -     4.26: 1125
        4.26 -     5.69: 90
        5.69 -     7.11: 7
  Bond angle restraints: 17966
  Sorted by residual:
  angle pdb=" C   PRO B 639 "
        pdb=" N   GLY B 640 "
        pdb=" CA  GLY B 640 "
      ideal   model   delta    sigma   weight residual
     121.82  125.91   -4.09 8.40e-01 1.42e+00 2.38e+01
  angle pdb=" C   GLU A 562 "
        pdb=" N   GLY A 563 "
        pdb=" CA  GLY A 563 "
      ideal   model   delta    sigma   weight residual
     119.92  124.44   -4.52 9.60e-01 1.09e+00 2.22e+01
  angle pdb=" C   PRO A 639 "
        pdb=" N   GLY A 640 "
        pdb=" CA  GLY A 640 "
      ideal   model   delta    sigma   weight residual
     121.82  125.77   -3.95 8.40e-01 1.42e+00 2.21e+01
  angle pdb=" N   PRO B 638 "
        pdb=" CA  PRO B 638 "
        pdb=" CB  PRO B 638 "
      ideal   model   delta    sigma   weight residual
     103.19  105.82   -2.63 5.60e-01 3.19e+00 2.21e+01
  angle pdb=" OE1 GLN A 324 "
        pdb=" CD  GLN A 324 "
        pdb=" NE2 GLN A 324 "
      ideal   model   delta    sigma   weight residual
     122.60  118.32    4.28 1.00e+00 1.00e+00 1.83e+01
  ... (remaining 17961 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.50: 7522
       16.50 -    32.99: 358
       32.99 -    49.49: 69
       49.49 -    65.99: 14
       65.99 -    82.48: 9
  Dihedral angle restraints: 7972
    sinusoidal: 3098
      harmonic: 4874
  Sorted by residual:
  dihedral pdb=" CA  ALA B  30 "
           pdb=" C   ALA B  30 "
           pdb=" N   ILE B  31 "
           pdb=" CA  ILE B  31 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.89   24.11     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  ALA A  30 "
           pdb=" C   ALA A  30 "
           pdb=" N   ILE A  31 "
           pdb=" CA  ILE A  31 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.21   23.79     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" CA  ALA B 205 "
           pdb=" C   ALA B 205 "
           pdb=" N   ILE B 206 "
           pdb=" CA  ILE B 206 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.83   21.17     0      5.00e+00 4.00e-02 1.79e+01
  ... (remaining 7969 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1180
       0.067 -    0.134: 626
       0.134 -    0.201: 172
       0.201 -    0.268: 6
       0.268 -    0.335: 4
  Chirality restraints: 1988
  Sorted by residual:
  chirality pdb=" CB  THR B 730 "
            pdb=" CA  THR B 730 "
            pdb=" OG1 THR B 730 "
            pdb=" CG2 THR B 730 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.22    0.33 2.00e-01 2.50e+01 2.80e+00
  chirality pdb=" CA  ASP A 691 "
            pdb=" N   ASP A 691 "
            pdb=" C   ASP A 691 "
            pdb=" CB  ASP A 691 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.53e+00
  chirality pdb=" CB  THR A 730 "
            pdb=" CA  THR A 730 "
            pdb=" OG1 THR A 730 "
            pdb=" CG2 THR A 730 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.26    0.29 2.00e-01 2.50e+01 2.16e+00
  ... (remaining 1985 not shown)

  Planarity restraints: 2340
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 298 "    0.112 2.00e-02 2.50e+03   6.20e-02 7.68e+01
        pdb=" CG  TYR B 298 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 298 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 298 "   -0.054 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 298 "   -0.038 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 298 "   -0.032 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 298 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR B 298 "    0.097 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 298 "   -0.108 2.00e-02 2.50e+03   5.96e-02 7.10e+01
        pdb=" CG  TYR A 298 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 298 "    0.049 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 298 "    0.049 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 298 "    0.035 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 298 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 298 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 298 "   -0.093 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 626 "    0.050 2.00e-02 2.50e+03   2.59e-02 1.34e+01
        pdb=" CG  TYR B 626 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 626 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 626 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 626 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 626 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 626 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR B 626 "    0.035 2.00e-02 2.50e+03
  ... (remaining 2337 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 43
        2.51 -     3.11: 8925
        3.11 -     3.70: 20583
        3.70 -     4.30: 31432
        4.30 -     4.90: 51120
  Nonbonded interactions: 112103
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A  46 "
            pdb=" NH2 ARG A  80 "
     model   vdw
     1.910 3.120
  nonbonded pdb=" OE1 GLN A 143 "
            pdb=" NH1 ARG A 215 "
     model   vdw
     2.098 3.120
  nonbonded pdb=" OE1 GLN B 143 "
            pdb=" NH1 ARG B 215 "
     model   vdw
     2.144 3.120
  nonbonded pdb=" OE1 GLU B  46 "
            pdb=" NH2 ARG B  80 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" NZ  LYS A 630 "
            pdb=" OD2 ASP A 634 "
     model   vdw
     2.287 3.120
  ... (remaining 112098 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             11.390
  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:          0.710
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     33.280
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5680
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      :  0.012   0.069  13242  Z= 0.741
  Angle     :  1.489   7.107  17966  Z= 0.997
  Chirality :  0.079   0.335   1988
  Planarity :  0.010   0.080   2340
  Dihedral  : 10.945  82.485   4836
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.78 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  1.21 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.19), residues: 1690
  helix: -0.11 (0.18), residues: 676
  sheet: -0.11 (0.32), residues: 212
  loop :  0.16 (0.21), residues: 802

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.009   TRP B 733 
 HIS   0.006   0.002   HIS B 473 
 PHE   0.042   0.007   PHE A 169 
 TYR   0.112   0.011   TYR B 298 
 ARG   0.008   0.002   ARG B 490 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17279 (  602)
  hydrogen bonds       : angle       7.18858 ( 1728)
  covalent geometry    : bond        0.01248 (13242)
  covalent geometry    : angle       1.48859 (17966)

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

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

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  444 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 438
  time to evaluate  : 1.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.7541 (mt0) cc_final: 0.7265 (tp40)
REVERT: A  107 LEU cc_start: 0.9432 (tp) cc_final: 0.8835 (tp)
REVERT: A  111 CYS cc_start: 0.8598 (m) cc_final: 0.8384 (m)
REVERT: A  179 TYR cc_start: 0.8408 (m-80) cc_final: 0.8014 (m-10)
REVERT: A  197 MET cc_start: 0.8142 (mtp) cc_final: 0.7591 (mmt)
REVERT: A  220 LYS cc_start: 0.8950 (tptt) cc_final: 0.7379 (tppt)
REVERT: A  253 PHE cc_start: 0.7546 (t80) cc_final: 0.7333 (t80)
REVERT: A  263 ILE cc_start: 0.7546 (mt) cc_final: 0.6905 (mt)
REVERT: A  270 VAL cc_start: 0.8475 (t) cc_final: 0.8189 (p)
REVERT: A  294 MET cc_start: 0.8355 (mtm) cc_final: 0.7875 (mtm)
REVERT: A  445 LEU cc_start: 0.8222 (tp) cc_final: 0.7122 (tp)
REVERT: A  579 THR cc_start: 0.8131 (m) cc_final: 0.7635 (p)
REVERT: A  589 LEU cc_start: 0.9196 (mt) cc_final: 0.8938 (mt)
REVERT: A  649 TRP cc_start: 0.5269 (t-100) cc_final: 0.4601 (t60)
REVERT: A  733 TRP cc_start: 0.6665 (t60) cc_final: 0.6317 (t60)
REVERT: A  820 SER cc_start: 0.8880 (m) cc_final: 0.8557 (p)
REVERT: B   92 LEU cc_start: 0.7797 (mt) cc_final: 0.7592 (mt)
REVERT: B  109 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7467 (mt-10)
REVERT: B  179 TYR cc_start: 0.8385 (m-80) cc_final: 0.7803 (m-10)
REVERT: B  263 ILE cc_start: 0.7663 (mt) cc_final: 0.7256 (mt)
REVERT: B  270 VAL cc_start: 0.8754 (t) cc_final: 0.8519 (p)
REVERT: B  294 MET cc_start: 0.8516 (mtm) cc_final: 0.7957 (mtm)
REVERT: B  360 MET cc_start: 0.8745 (mmm) cc_final: 0.8430 (mmt)
REVERT: B  445 LEU cc_start: 0.8106 (tp) cc_final: 0.7127 (tp)
REVERT: B  579 THR cc_start: 0.8056 (m) cc_final: 0.7586 (p)
REVERT: B  589 LEU cc_start: 0.9275 (mt) cc_final: 0.8958 (mt)
REVERT: B  733 TRP cc_start: 0.6612 (t60) cc_final: 0.6144 (t60)
REVERT: B  785 HIS cc_start: 0.6494 (t70) cc_final: 0.4764 (t70)
REVERT: B  796 LEU cc_start: 0.6866 (mt) cc_final: 0.6582 (mt)
  outliers start: 6
  outliers final: 2
  residues processed: 444
  average time/residue: 0.2817
  time to fit residues: 172.1610
Evaluate side-chains
  240 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 238
  time to evaluate  : 1.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    6.9990
   chunk 127 optimal weight:    4.9990
   chunk 70 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 131 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 152 optimal weight:    6.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 371 HIS
A 464 GLN
A 705 HIS
B 602 HIS
B 771 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.121522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.093778 restraints weight = 45047.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.096569 restraints weight = 34708.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.098703 restraints weight = 27935.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.3688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13242  Z= 0.180
  Angle     :  0.662   7.560  17966  Z= 0.348
  Chirality :  0.047   0.280   1988
  Planarity :  0.005   0.057   2340
  Dihedral  :  4.774  16.928   1812
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.13 %
    Favored  : 97.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.20), residues: 1690
  helix:  0.80 (0.19), residues: 716
  sheet:  0.18 (0.33), residues: 242
  loop :  0.73 (0.24), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP A 627 
 HIS   0.009   0.002   HIS A 314 
 PHE   0.021   0.002   PHE B 311 
 TYR   0.021   0.002   TYR A 298 
 ARG   0.006   0.001   ARG B 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04494 (  602)
  hydrogen bonds       : angle       5.58066 ( 1728)
  covalent geometry    : bond        0.00391 (13242)
  covalent geometry    : angle       0.66231 (17966)

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

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

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 314
  time to evaluate  : 1.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 LEU cc_start: 0.9569 (tp) cc_final: 0.9119 (tp)
REVERT: A  108 LEU cc_start: 0.9408 (mt) cc_final: 0.9195 (mt)
REVERT: A  109 GLU cc_start: 0.8649 (tt0) cc_final: 0.7624 (tt0)
REVERT: A  145 TRP cc_start: 0.7412 (m-10) cc_final: 0.7169 (m-10)
REVERT: A  197 MET cc_start: 0.8901 (mtp) cc_final: 0.8266 (mmt)
REVERT: A  220 LYS cc_start: 0.9650 (tptt) cc_final: 0.9425 (tppt)
REVERT: A  225 MET cc_start: 0.7395 (tpp) cc_final: 0.7145 (tpp)
REVERT: A  227 MET cc_start: 0.8506 (mmp) cc_final: 0.8290 (mmp)
REVERT: A  263 ILE cc_start: 0.8243 (mt) cc_final: 0.7910 (mt)
REVERT: A  270 VAL cc_start: 0.9328 (t) cc_final: 0.9004 (p)
REVERT: A  370 MET cc_start: 0.8551 (mtt) cc_final: 0.8262 (mtt)
REVERT: A  462 GLU cc_start: 0.9181 (tt0) cc_final: 0.8625 (tt0)
REVERT: A  518 TYR cc_start: 0.8556 (m-80) cc_final: 0.7997 (m-80)
REVERT: A  532 LEU cc_start: 0.9411 (mm) cc_final: 0.9086 (mt)
REVERT: A  575 PHE cc_start: 0.8749 (m-10) cc_final: 0.8499 (m-80)
REVERT: A  767 HIS cc_start: 0.8818 (t70) cc_final: 0.8524 (t70)
REVERT: A  820 SER cc_start: 0.9426 (m) cc_final: 0.9117 (p)
REVERT: B   57 MET cc_start: 0.8369 (mpp) cc_final: 0.7065 (mpp)
REVERT: B   92 LEU cc_start: 0.8578 (mt) cc_final: 0.8304 (mt)
REVERT: B  107 LEU cc_start: 0.9687 (tp) cc_final: 0.9392 (tp)
REVERT: B  111 CYS cc_start: 0.9354 (m) cc_final: 0.9154 (m)
REVERT: B  155 MET cc_start: 0.7693 (mtm) cc_final: 0.7393 (mmm)
REVERT: B  197 MET cc_start: 0.8842 (mmm) cc_final: 0.8373 (mmm)
REVERT: B  263 ILE cc_start: 0.8392 (mt) cc_final: 0.8178 (mt)
REVERT: B  270 VAL cc_start: 0.9472 (t) cc_final: 0.9166 (p)
REVERT: B  294 MET cc_start: 0.8958 (mtm) cc_final: 0.8393 (mmm)
REVERT: B  333 MET cc_start: 0.7219 (mmm) cc_final: 0.6625 (mtp)
REVERT: B  532 LEU cc_start: 0.9379 (mm) cc_final: 0.9126 (mt)
REVERT: B  702 ILE cc_start: 0.9381 (mp) cc_final: 0.9048 (mp)
REVERT: B  760 LEU cc_start: 0.7830 (tp) cc_final: 0.7069 (mm)
REVERT: B  767 HIS cc_start: 0.8390 (t70) cc_final: 0.8153 (t70)
REVERT: B  770 LEU cc_start: 0.8904 (mt) cc_final: 0.8688 (mt)
REVERT: B  796 LEU cc_start: 0.8480 (mt) cc_final: 0.8034 (mt)
  outliers start: 3
  outliers final: 0
  residues processed: 314
  average time/residue: 0.2461
  time to fit residues: 111.2807
Evaluate side-chains
  215 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 1.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 89 optimal weight:    8.9990
   chunk 20 optimal weight:    0.6980
   chunk 77 optimal weight:   10.0000
   chunk 70 optimal weight:    6.9990
   chunk 84 optimal weight:   10.0000
   chunk 48 optimal weight:    8.9990
   chunk 87 optimal weight:    4.9990
   chunk 109 optimal weight:    8.9990
   chunk 138 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 117 optimal weight:    0.4980
   overall best weight:    3.4386

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

Flipped N/Q/H residues before XYZ refinement:
A 195 GLN
** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 350 ASN
A 705 HIS
** A 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 350 ASN
B 371 HIS
B 602 HIS
** B 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.110441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.085723 restraints weight = 48394.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.088221 restraints weight = 36617.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.090083 restraints weight = 29325.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.5389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  13242  Z= 0.232
  Angle     :  0.718   8.322  17966  Z= 0.377
  Chirality :  0.046   0.163   1988
  Planarity :  0.006   0.048   2340
  Dihedral  :  5.016  24.104   1812
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 17.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.05 %
    Favored  : 96.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.20), residues: 1690
  helix:  0.38 (0.19), residues: 714
  sheet:  0.12 (0.34), residues: 228
  loop :  0.61 (0.24), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP A 859 
 HIS   0.009   0.002   HIS A 423 
 PHE   0.035   0.002   PHE A 311 
 TYR   0.016   0.002   TYR A 112 
 ARG   0.008   0.001   ARG A 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04837 (  602)
  hydrogen bonds       : angle       5.95952 ( 1728)
  covalent geometry    : bond        0.00492 (13242)
  covalent geometry    : angle       0.71768 (17966)

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

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

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 261
  time to evaluate  : 1.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 LEU cc_start: 0.9501 (tp) cc_final: 0.9259 (tp)
REVERT: A  108 LEU cc_start: 0.9514 (mt) cc_final: 0.9299 (mt)
REVERT: A  111 CYS cc_start: 0.9493 (m) cc_final: 0.9279 (m)
REVERT: A  113 GLU cc_start: 0.8557 (mp0) cc_final: 0.8123 (mm-30)
REVERT: A  145 TRP cc_start: 0.7831 (m-10) cc_final: 0.7564 (m-10)
REVERT: A  197 MET cc_start: 0.9088 (mtp) cc_final: 0.8676 (mmm)
REVERT: A  220 LYS cc_start: 0.9638 (tptt) cc_final: 0.9364 (tppt)
REVERT: A  225 MET cc_start: 0.7777 (tpp) cc_final: 0.7520 (tpp)
REVERT: A  263 ILE cc_start: 0.8361 (mt) cc_final: 0.8091 (mt)
REVERT: A  294 MET cc_start: 0.9416 (mtt) cc_final: 0.8945 (mmt)
REVERT: A  360 MET cc_start: 0.9255 (tpp) cc_final: 0.8826 (tpp)
REVERT: A  518 TYR cc_start: 0.8658 (m-80) cc_final: 0.8079 (m-80)
REVERT: A  579 THR cc_start: 0.9266 (p) cc_final: 0.8966 (p)
REVERT: A  582 GLN cc_start: 0.9343 (mt0) cc_final: 0.8885 (mt0)
REVERT: A  602 HIS cc_start: 0.8531 (t-90) cc_final: 0.8314 (t70)
REVERT: A  733 TRP cc_start: 0.8224 (t60) cc_final: 0.7767 (t60)
REVERT: A  767 HIS cc_start: 0.8902 (t70) cc_final: 0.8702 (t70)
REVERT: A  820 SER cc_start: 0.9407 (m) cc_final: 0.9175 (p)
REVERT: A  844 VAL cc_start: 0.8780 (m) cc_final: 0.8483 (p)
REVERT: A  855 VAL cc_start: 0.9229 (p) cc_final: 0.8906 (p)
REVERT: B   57 MET cc_start: 0.8662 (mpp) cc_final: 0.8215 (mpp)
REVERT: B   92 LEU cc_start: 0.8944 (mt) cc_final: 0.8714 (mt)
REVERT: B   99 MET cc_start: 0.8461 (mmp) cc_final: 0.8118 (tpp)
REVERT: B  107 LEU cc_start: 0.9681 (tp) cc_final: 0.9379 (tp)
REVERT: B  108 LEU cc_start: 0.9592 (mt) cc_final: 0.9301 (mt)
REVERT: B  150 ASP cc_start: 0.8468 (m-30) cc_final: 0.8186 (m-30)
REVERT: B  197 MET cc_start: 0.8900 (mmm) cc_final: 0.8586 (mmm)
REVERT: B  263 ILE cc_start: 0.8390 (mt) cc_final: 0.8131 (mt)
REVERT: B  417 MET cc_start: 0.8798 (ptp) cc_final: 0.8472 (ptp)
REVERT: B  528 MET cc_start: 0.8311 (pmm) cc_final: 0.7152 (pmm)
REVERT: B  577 CYS cc_start: 0.9035 (m) cc_final: 0.8588 (t)
REVERT: B  579 THR cc_start: 0.9193 (p) cc_final: 0.8849 (p)
REVERT: B  582 GLN cc_start: 0.9291 (mt0) cc_final: 0.9012 (mt0)
REVERT: B  592 MET cc_start: 0.9489 (mmp) cc_final: 0.9178 (tpp)
REVERT: B  616 LEU cc_start: 0.6805 (mp) cc_final: 0.6577 (mp)
REVERT: B  844 VAL cc_start: 0.8633 (m) cc_final: 0.8357 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 262
  average time/residue: 0.2282
  time to fit residues: 90.6264
Evaluate side-chains
  188 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 1.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 150 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 11 optimal weight:    6.9990
   chunk 148 optimal weight:    0.6980
   chunk 71 optimal weight:    4.9990
   chunk 51 optimal weight:   20.0000
   chunk 45 optimal weight:    0.7980
   chunk 160 optimal weight:    3.9990
   chunk 113 optimal weight:    8.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 350 ASN
** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 HIS
A 806 GLN
B 195 GLN
B 350 ASN
B 655 GLN
B 806 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.113515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.088558 restraints weight = 45352.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.091211 restraints weight = 34041.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.093257 restraints weight = 26890.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.5582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13242  Z= 0.123
  Angle     :  0.595  11.411  17966  Z= 0.302
  Chirality :  0.045   0.193   1988
  Planarity :  0.004   0.045   2340
  Dihedral  :  4.483  16.343   1812
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.20), residues: 1690
  helix:  0.92 (0.19), residues: 712
  sheet: -0.06 (0.33), residues: 242
  loop :  0.66 (0.24), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 865 
 HIS   0.005   0.001   HIS A 371 
 PHE   0.027   0.002   PHE A 818 
 TYR   0.017   0.001   TYR A 704 
 ARG   0.005   0.000   ARG B 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03922 (  602)
  hydrogen bonds       : angle       5.42187 ( 1728)
  covalent geometry    : bond        0.00280 (13242)
  covalent geometry    : angle       0.59479 (17966)

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

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

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 1.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 MET cc_start: 0.8672 (mpp) cc_final: 0.8097 (mpp)
REVERT: A   96 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8669 (mp10)
REVERT: A  107 LEU cc_start: 0.9458 (tp) cc_final: 0.9226 (tp)
REVERT: A  108 LEU cc_start: 0.9573 (mt) cc_final: 0.9368 (mt)
REVERT: A  197 MET cc_start: 0.9040 (mtp) cc_final: 0.8643 (mmm)
REVERT: A  220 LYS cc_start: 0.9647 (tptt) cc_final: 0.9345 (tppt)
REVERT: A  294 MET cc_start: 0.9489 (mtt) cc_final: 0.9164 (mmm)
REVERT: A  333 MET cc_start: 0.7210 (mtp) cc_final: 0.6783 (mtp)
REVERT: A  370 MET cc_start: 0.8901 (mtt) cc_final: 0.8478 (mtt)
REVERT: A  447 THR cc_start: 0.8396 (p) cc_final: 0.8123 (p)
REVERT: A  609 CYS cc_start: 0.8088 (m) cc_final: 0.7600 (m)
REVERT: A  733 TRP cc_start: 0.8047 (t60) cc_final: 0.7592 (t60)
REVERT: A  767 HIS cc_start: 0.8911 (t70) cc_final: 0.8656 (t-170)
REVERT: A  820 SER cc_start: 0.9431 (m) cc_final: 0.9205 (p)
REVERT: B   92 LEU cc_start: 0.8973 (mt) cc_final: 0.8743 (mt)
REVERT: B   99 MET cc_start: 0.8452 (mmp) cc_final: 0.8233 (tpp)
REVERT: B  107 LEU cc_start: 0.9676 (tp) cc_final: 0.9367 (tp)
REVERT: B  108 LEU cc_start: 0.9597 (mt) cc_final: 0.9297 (mt)
REVERT: B  113 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8168 (mt-10)
REVERT: B  150 ASP cc_start: 0.8429 (m-30) cc_final: 0.8212 (m-30)
REVERT: B  187 LEU cc_start: 0.9608 (mm) cc_final: 0.9371 (tp)
REVERT: B  197 MET cc_start: 0.8965 (mmm) cc_final: 0.8594 (mmm)
REVERT: B  294 MET cc_start: 0.9454 (mtt) cc_final: 0.8884 (mmm)
REVERT: B  333 MET cc_start: 0.7001 (mtp) cc_final: 0.6273 (mtp)
REVERT: B  360 MET cc_start: 0.9485 (mmm) cc_final: 0.9154 (mmm)
REVERT: B  484 LEU cc_start: 0.8459 (tt) cc_final: 0.8029 (tp)
REVERT: B  577 CYS cc_start: 0.9056 (m) cc_final: 0.8640 (t)
REVERT: B  579 THR cc_start: 0.9280 (p) cc_final: 0.8957 (p)
REVERT: B  581 ILE cc_start: 0.9274 (mt) cc_final: 0.9057 (mt)
REVERT: B  582 GLN cc_start: 0.9367 (mt0) cc_final: 0.8979 (mt0)
REVERT: B  592 MET cc_start: 0.9475 (mmp) cc_final: 0.9206 (tpp)
REVERT: B  616 LEU cc_start: 0.6654 (mp) cc_final: 0.6443 (mp)
REVERT: B  733 TRP cc_start: 0.8084 (t60) cc_final: 0.7804 (t60)
REVERT: B  767 HIS cc_start: 0.8405 (t70) cc_final: 0.7956 (t70)
REVERT: B  851 LEU cc_start: 0.8197 (mt) cc_final: 0.7925 (mt)
REVERT: B  855 VAL cc_start: 0.9105 (p) cc_final: 0.8743 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 268
  average time/residue: 0.2543
  time to fit residues: 101.6541
Evaluate side-chains
  192 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 93 optimal weight:    0.3980
   chunk 10 optimal weight:   10.0000
   chunk 123 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 98 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   chunk 44 optimal weight:    9.9990
   chunk 151 optimal weight:    5.9990
   chunk 40 optimal weight:    9.9990
   chunk 150 optimal weight:    0.3980
   overall best weight:    2.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 350 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 466 HIS
A 582 GLN
A 705 HIS
B 350 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 705 HIS
** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.108847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.084613 restraints weight = 47211.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.087083 restraints weight = 35364.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.088923 restraints weight = 28006.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.6438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13242  Z= 0.176
  Angle     :  0.636   9.051  17966  Z= 0.325
  Chirality :  0.045   0.164   1988
  Planarity :  0.005   0.044   2340
  Dihedral  :  4.562  17.504   1812
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.20), residues: 1690
  helix:  0.80 (0.19), residues: 704
  sheet: -0.36 (0.32), residues: 266
  loop :  0.66 (0.24), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 859 
 HIS   0.005   0.001   HIS B 785 
 PHE   0.020   0.002   PHE A 818 
 TYR   0.014   0.002   TYR B 112 
 ARG   0.004   0.001   ARG A 451 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04112 (  602)
  hydrogen bonds       : angle       5.64150 ( 1728)
  covalent geometry    : bond        0.00381 (13242)
  covalent geometry    : angle       0.63557 (17966)

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

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

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 1.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.8997 (mt) cc_final: 0.8672 (mt)
REVERT: A   99 MET cc_start: 0.8346 (mmp) cc_final: 0.8014 (mmm)
REVERT: A  108 LEU cc_start: 0.9587 (mt) cc_final: 0.9341 (mt)
REVERT: A  145 TRP cc_start: 0.7551 (m-10) cc_final: 0.7295 (m-10)
REVERT: A  197 MET cc_start: 0.9105 (mtp) cc_final: 0.8707 (mmm)
REVERT: A  220 LYS cc_start: 0.9639 (tptt) cc_final: 0.9340 (tppt)
REVERT: A  263 ILE cc_start: 0.8335 (mt) cc_final: 0.8135 (mt)
REVERT: A  294 MET cc_start: 0.9544 (mtt) cc_final: 0.9046 (mmt)
REVERT: A  370 MET cc_start: 0.9088 (mtt) cc_final: 0.8864 (mtt)
REVERT: A  410 MET cc_start: 0.8789 (mmt) cc_final: 0.8543 (mmt)
REVERT: A  448 TYR cc_start: 0.8806 (t80) cc_final: 0.8604 (t80)
REVERT: A  462 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8404 (tm-30)
REVERT: A  528 MET cc_start: 0.7851 (pmm) cc_final: 0.7509 (pmm)
REVERT: A  582 GLN cc_start: 0.9643 (tt0) cc_final: 0.9085 (tp40)
REVERT: A  604 MET cc_start: 0.8475 (mpp) cc_final: 0.8134 (mpp)
REVERT: A  616 LEU cc_start: 0.6768 (mp) cc_final: 0.6447 (mp)
REVERT: A  727 LYS cc_start: 0.7155 (mttt) cc_final: 0.6913 (mttt)
REVERT: A  733 TRP cc_start: 0.8057 (t60) cc_final: 0.7807 (t60)
REVERT: A  767 HIS cc_start: 0.8826 (t70) cc_final: 0.8401 (t70)
REVERT: A  770 LEU cc_start: 0.8839 (mt) cc_final: 0.8560 (mt)
REVERT: A  844 VAL cc_start: 0.8843 (m) cc_final: 0.8616 (p)
REVERT: B   92 LEU cc_start: 0.9015 (mt) cc_final: 0.8804 (mt)
REVERT: B  108 LEU cc_start: 0.9600 (mt) cc_final: 0.9382 (mt)
REVERT: B  113 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8240 (mt-10)
REVERT: B  197 MET cc_start: 0.8971 (mmm) cc_final: 0.8607 (mmm)
REVERT: B  294 MET cc_start: 0.9497 (mtt) cc_final: 0.9049 (mmm)
REVERT: B  333 MET cc_start: 0.7570 (mtp) cc_final: 0.7032 (mtp)
REVERT: B  360 MET cc_start: 0.9527 (mmm) cc_final: 0.9030 (tpp)
REVERT: B  417 MET cc_start: 0.8818 (ptp) cc_final: 0.8617 (ptp)
REVERT: B  449 SER cc_start: 0.7980 (m) cc_final: 0.7716 (p)
REVERT: B  577 CYS cc_start: 0.9108 (m) cc_final: 0.8719 (t)
REVERT: B  579 THR cc_start: 0.9284 (p) cc_final: 0.8936 (p)
REVERT: B  581 ILE cc_start: 0.9279 (mt) cc_final: 0.9071 (mt)
REVERT: B  582 GLN cc_start: 0.9363 (mt0) cc_final: 0.8938 (mt0)
REVERT: B  592 MET cc_start: 0.9475 (mmp) cc_final: 0.9202 (tpp)
REVERT: B  616 LEU cc_start: 0.6671 (mp) cc_final: 0.6444 (mp)
REVERT: B  727 LYS cc_start: 0.7175 (mttt) cc_final: 0.6967 (mmtt)
REVERT: B  733 TRP cc_start: 0.8240 (t60) cc_final: 0.7930 (t60)
REVERT: B  767 HIS cc_start: 0.8530 (t70) cc_final: 0.8080 (t70)
REVERT: B  770 LEU cc_start: 0.8962 (mt) cc_final: 0.8679 (mt)
REVERT: B  785 HIS cc_start: 0.7370 (t-90) cc_final: 0.7168 (t-90)
REVERT: B  844 VAL cc_start: 0.8778 (m) cc_final: 0.8542 (p)
REVERT: B  855 VAL cc_start: 0.9125 (p) cc_final: 0.8839 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.2280
  time to fit residues: 84.3190
Evaluate side-chains
  177 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 35 optimal weight:   10.0000
   chunk 151 optimal weight:   10.0000
   chunk 104 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   chunk 132 optimal weight:   10.0000
   chunk 96 optimal weight:    4.9990
   chunk 95 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 133 optimal weight:    0.9980
   chunk 159 optimal weight:    6.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 HIS
A 785 HIS
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 705 HIS
** B 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.100239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.077761 restraints weight = 51305.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.080109 restraints weight = 38056.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.081816 restraints weight = 29928.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.8052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  13242  Z= 0.287
  Angle     :  0.805  10.745  17966  Z= 0.415
  Chirality :  0.048   0.249   1988
  Planarity :  0.006   0.065   2340
  Dihedral  :  5.377  23.464   1812
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 23.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.20), residues: 1690
  helix:  0.05 (0.18), residues: 706
  sheet:  0.31 (0.39), residues: 192
  loop :  0.02 (0.23), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP A 859 
 HIS   0.010   0.002   HIS B 705 
 PHE   0.023   0.003   PHE A 501 
 TYR   0.027   0.003   TYR A  38 
 ARG   0.007   0.001   ARG B 732 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04837 (  602)
  hydrogen bonds       : angle       6.50104 ( 1728)
  covalent geometry    : bond        0.00595 (13242)
  covalent geometry    : angle       0.80543 (17966)

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

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

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 1.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9260 (mt) cc_final: 0.8942 (mt)
REVERT: A   96 GLN cc_start: 0.9074 (mp10) cc_final: 0.8859 (mp10)
REVERT: A   99 MET cc_start: 0.8516 (mmp) cc_final: 0.8260 (mmm)
REVERT: A  107 LEU cc_start: 0.9552 (tp) cc_final: 0.9342 (tp)
REVERT: A  108 LEU cc_start: 0.9599 (mt) cc_final: 0.9323 (mt)
REVERT: A  113 GLU cc_start: 0.8693 (mp0) cc_final: 0.8368 (mp0)
REVERT: A  197 MET cc_start: 0.9192 (mtp) cc_final: 0.8731 (tpp)
REVERT: A  220 LYS cc_start: 0.9588 (tptt) cc_final: 0.9334 (tppt)
REVERT: A  294 MET cc_start: 0.9592 (mtt) cc_final: 0.9384 (mtp)
REVERT: A  303 LEU cc_start: 0.8569 (tp) cc_final: 0.8152 (tt)
REVERT: A  360 MET cc_start: 0.9223 (tpp) cc_final: 0.8677 (tmm)
REVERT: A  448 TYR cc_start: 0.9205 (t80) cc_final: 0.8729 (t80)
REVERT: A  518 TYR cc_start: 0.8920 (m-80) cc_final: 0.8450 (m-10)
REVERT: A  592 MET cc_start: 0.9567 (mmm) cc_final: 0.9034 (tpp)
REVERT: A  604 MET cc_start: 0.8264 (mpp) cc_final: 0.8044 (mpp)
REVERT: A  727 LYS cc_start: 0.7694 (mttt) cc_final: 0.7412 (mmtt)
REVERT: A  733 TRP cc_start: 0.7981 (t60) cc_final: 0.7775 (t60)
REVERT: A  767 HIS cc_start: 0.8802 (t70) cc_final: 0.8353 (t70)
REVERT: A  770 LEU cc_start: 0.9050 (mt) cc_final: 0.8786 (mt)
REVERT: B   57 MET cc_start: 0.8591 (mpp) cc_final: 0.8193 (mpp)
REVERT: B   99 MET cc_start: 0.8534 (tpp) cc_final: 0.8257 (tpp)
REVERT: B  108 LEU cc_start: 0.9680 (mt) cc_final: 0.9427 (mt)
REVERT: B  113 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8334 (mt-10)
REVERT: B  155 MET cc_start: 0.8864 (mtp) cc_final: 0.8627 (mtp)
REVERT: B  197 MET cc_start: 0.9076 (mmm) cc_final: 0.8565 (mmm)
REVERT: B  303 LEU cc_start: 0.8487 (tp) cc_final: 0.8086 (tt)
REVERT: B  333 MET cc_start: 0.8137 (mtp) cc_final: 0.7823 (mtp)
REVERT: B  495 LEU cc_start: 0.9357 (mt) cc_final: 0.9130 (mm)
REVERT: B  592 MET cc_start: 0.9519 (mmp) cc_final: 0.9274 (tpp)
REVERT: B  727 LYS cc_start: 0.7745 (mttt) cc_final: 0.7505 (mmtt)
REVERT: B  732 ARG cc_start: 0.8746 (mpp-170) cc_final: 0.8477 (mpt180)
REVERT: B  770 LEU cc_start: 0.9102 (mt) cc_final: 0.8853 (mt)
REVERT: B  785 HIS cc_start: 0.7192 (t-90) cc_final: 0.6965 (t-90)
REVERT: B  855 VAL cc_start: 0.9215 (p) cc_final: 0.8871 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.2601
  time to fit residues: 93.2988
Evaluate side-chains
  179 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 1.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 102 optimal weight:    5.9990
   chunk 103 optimal weight:    1.9990
   chunk 85 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   chunk 91 optimal weight:    2.9990
   chunk 74 optimal weight:    9.9990
   chunk 28 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 314 HIS
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 655 GLN
** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 759 ASN
** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.102876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.079810 restraints weight = 49425.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.082170 restraints weight = 36772.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.083993 restraints weight = 28866.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.8339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13242  Z= 0.175
  Angle     :  0.678   9.310  17966  Z= 0.345
  Chirality :  0.046   0.200   1988
  Planarity :  0.005   0.051   2340
  Dihedral  :  4.971  18.227   1812
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 18.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.21), residues: 1690
  helix:  0.43 (0.19), residues: 708
  sheet: -0.60 (0.35), residues: 244
  loop :  0.39 (0.24), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRP B 733 
 HIS   0.007   0.001   HIS B 785 
 PHE   0.021   0.002   PHE B 683 
 TYR   0.021   0.002   TYR A  38 
 ARG   0.005   0.000   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04147 (  602)
  hydrogen bonds       : angle       5.93528 ( 1728)
  covalent geometry    : bond        0.00379 (13242)
  covalent geometry    : angle       0.67805 (17966)

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

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

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 1.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 MET cc_start: 0.8744 (mpp) cc_final: 0.7761 (mpp)
REVERT: A   92 LEU cc_start: 0.9185 (mt) cc_final: 0.8910 (mt)
REVERT: A   96 GLN cc_start: 0.8903 (mp10) cc_final: 0.8670 (mp10)
REVERT: A  197 MET cc_start: 0.9174 (mtp) cc_final: 0.8948 (tpp)
REVERT: A  220 LYS cc_start: 0.9608 (tptt) cc_final: 0.9355 (tppt)
REVERT: A  290 GLN cc_start: 0.8802 (mt0) cc_final: 0.8409 (mp10)
REVERT: A  303 LEU cc_start: 0.8559 (tp) cc_final: 0.8157 (tt)
REVERT: A  333 MET cc_start: 0.8092 (mtp) cc_final: 0.7847 (mtp)
REVERT: A  360 MET cc_start: 0.9410 (tpp) cc_final: 0.8751 (tmm)
REVERT: A  470 MET cc_start: 0.8370 (pmm) cc_final: 0.7905 (pmm)
REVERT: A  495 LEU cc_start: 0.9397 (mt) cc_final: 0.9115 (mm)
REVERT: A  592 MET cc_start: 0.9581 (mmm) cc_final: 0.9097 (tpp)
REVERT: A  727 LYS cc_start: 0.7731 (mttt) cc_final: 0.7459 (mmtt)
REVERT: A  733 TRP cc_start: 0.7946 (t60) cc_final: 0.7514 (t60)
REVERT: A  767 HIS cc_start: 0.8912 (t70) cc_final: 0.8499 (t70)
REVERT: A  770 LEU cc_start: 0.8986 (mt) cc_final: 0.8710 (mt)
REVERT: B   57 MET cc_start: 0.8653 (mpp) cc_final: 0.8139 (mpp)
REVERT: B   99 MET cc_start: 0.8469 (tpp) cc_final: 0.8175 (tpp)
REVERT: B  108 LEU cc_start: 0.9687 (mt) cc_final: 0.9472 (mt)
REVERT: B  113 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8411 (mt-10)
REVERT: B  197 MET cc_start: 0.9120 (mmm) cc_final: 0.8688 (mmm)
REVERT: B  225 MET cc_start: 0.8473 (mmm) cc_final: 0.8081 (mmm)
REVERT: B  290 GLN cc_start: 0.8682 (mt0) cc_final: 0.8351 (mp10)
REVERT: B  303 LEU cc_start: 0.8444 (tp) cc_final: 0.8039 (tt)
REVERT: B  360 MET cc_start: 0.9384 (mmp) cc_final: 0.8788 (mmt)
REVERT: B  470 MET cc_start: 0.7412 (mtm) cc_final: 0.6941 (pmm)
REVERT: B  495 LEU cc_start: 0.9367 (mt) cc_final: 0.9133 (mm)
REVERT: B  577 CYS cc_start: 0.9266 (m) cc_final: 0.9032 (p)
REVERT: B  592 MET cc_start: 0.9534 (mmp) cc_final: 0.9211 (tpp)
REVERT: B  684 MET cc_start: -0.1505 (mtt) cc_final: -0.1784 (mtt)
REVERT: B  727 LYS cc_start: 0.7711 (mttt) cc_final: 0.7490 (mmtt)
REVERT: B  767 HIS cc_start: 0.8528 (t70) cc_final: 0.8142 (t-170)
REVERT: B  770 LEU cc_start: 0.9046 (mt) cc_final: 0.8842 (mt)
REVERT: B  794 ARG cc_start: 0.9077 (ptt90) cc_final: 0.8764 (ptt90)
REVERT: B  855 VAL cc_start: 0.9085 (p) cc_final: 0.8706 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.2297
  time to fit residues: 82.2269
Evaluate side-chains
  188 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 1.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 145 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 59 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 117 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 314 HIS
** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 378 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.105091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.081347 restraints weight = 48747.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.083787 restraints weight = 36397.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.085428 restraints weight = 28931.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.8520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13242  Z= 0.136
  Angle     :  0.638  10.104  17966  Z= 0.323
  Chirality :  0.045   0.187   1988
  Planarity :  0.004   0.046   2340
  Dihedral  :  4.709  21.860   1812
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 16.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.21), residues: 1690
  helix:  0.61 (0.19), residues: 708
  sheet: -0.53 (0.34), residues: 252
  loop :  0.44 (0.24), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.065   0.003   TRP B 733 
 HIS   0.006   0.001   HIS B 785 
 PHE   0.021   0.002   PHE A 381 
 TYR   0.025   0.002   TYR A 112 
 ARG   0.006   0.000   ARG B 451 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03897 (  602)
  hydrogen bonds       : angle       5.70540 ( 1728)
  covalent geometry    : bond        0.00309 (13242)
  covalent geometry    : angle       0.63780 (17966)

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

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

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 1.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 MET cc_start: 0.8772 (mpp) cc_final: 0.7101 (mpp)
REVERT: A   96 GLN cc_start: 0.8905 (mp10) cc_final: 0.8680 (mp10)
REVERT: A  197 MET cc_start: 0.9153 (mtp) cc_final: 0.8681 (tpp)
REVERT: A  220 LYS cc_start: 0.9634 (tptt) cc_final: 0.9381 (tppt)
REVERT: A  290 GLN cc_start: 0.8803 (mt0) cc_final: 0.8442 (mp10)
REVERT: A  360 MET cc_start: 0.9403 (tpp) cc_final: 0.8981 (tpt)
REVERT: A  470 MET cc_start: 0.8355 (pmm) cc_final: 0.7885 (pmm)
REVERT: A  495 LEU cc_start: 0.9366 (mt) cc_final: 0.9089 (mm)
REVERT: A  513 GLU cc_start: 0.8411 (tp30) cc_final: 0.7943 (tp30)
REVERT: A  592 MET cc_start: 0.9538 (mmm) cc_final: 0.9098 (tpp)
REVERT: A  727 LYS cc_start: 0.7754 (mttt) cc_final: 0.7493 (mmtt)
REVERT: A  733 TRP cc_start: 0.7935 (t60) cc_final: 0.7605 (t60)
REVERT: A  767 HIS cc_start: 0.8941 (t70) cc_final: 0.8553 (t70)
REVERT: A  770 LEU cc_start: 0.8924 (mt) cc_final: 0.8656 (mt)
REVERT: A  854 MET cc_start: 0.9047 (ptp) cc_final: 0.8406 (pmm)
REVERT: B   57 MET cc_start: 0.8642 (mpp) cc_final: 0.8133 (mpp)
REVERT: B   99 MET cc_start: 0.8410 (tpp) cc_final: 0.8104 (tpp)
REVERT: B  108 LEU cc_start: 0.9673 (mt) cc_final: 0.9454 (mt)
REVERT: B  113 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8525 (mt-10)
REVERT: B  186 VAL cc_start: 0.9027 (t) cc_final: 0.8121 (t)
REVERT: B  197 MET cc_start: 0.9123 (mmm) cc_final: 0.8687 (mmm)
REVERT: B  225 MET cc_start: 0.8306 (mmm) cc_final: 0.7988 (mmm)
REVERT: B  290 GLN cc_start: 0.8707 (mt0) cc_final: 0.8342 (mp10)
REVERT: B  294 MET cc_start: 0.9389 (mmm) cc_final: 0.9128 (mmm)
REVERT: B  303 LEU cc_start: 0.8449 (tp) cc_final: 0.8042 (tt)
REVERT: B  313 CYS cc_start: 0.7817 (m) cc_final: 0.7387 (t)
REVERT: B  360 MET cc_start: 0.9278 (mmp) cc_final: 0.8714 (mmt)
REVERT: B  470 MET cc_start: 0.7440 (mtm) cc_final: 0.7020 (pmm)
REVERT: B  476 CYS cc_start: 0.9263 (m) cc_final: 0.9048 (m)
REVERT: B  573 ASN cc_start: 0.9081 (m-40) cc_final: 0.8725 (t0)
REVERT: B  577 CYS cc_start: 0.9348 (m) cc_final: 0.9101 (p)
REVERT: B  592 MET cc_start: 0.9492 (mmp) cc_final: 0.9196 (tpp)
REVERT: B  627 TRP cc_start: 0.8618 (m-90) cc_final: 0.8244 (m-90)
REVERT: B  649 TRP cc_start: 0.7707 (t-100) cc_final: 0.7259 (t-100)
REVERT: B  727 LYS cc_start: 0.7740 (mttt) cc_final: 0.7534 (mmtt)
REVERT: B  767 HIS cc_start: 0.8564 (t70) cc_final: 0.8099 (t70)
REVERT: B  770 LEU cc_start: 0.8915 (mt) cc_final: 0.8567 (mt)
REVERT: B  785 HIS cc_start: 0.7392 (t-90) cc_final: 0.7059 (t-90)
REVERT: B  855 VAL cc_start: 0.9077 (p) cc_final: 0.8759 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 256
  average time/residue: 0.2303
  time to fit residues: 87.0369
Evaluate side-chains
  199 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 144 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9980
   chunk 10 optimal weight:    8.9990
   chunk 100 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 104 optimal weight:   10.0000
   chunk 105 optimal weight:    0.5980
   chunk 19 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.104547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.081115 restraints weight = 48229.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.083599 restraints weight = 35968.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.085546 restraints weight = 27970.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.8716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13242  Z= 0.134
  Angle     :  0.641  10.046  17966  Z= 0.324
  Chirality :  0.046   0.212   1988
  Planarity :  0.005   0.045   2340
  Dihedral  :  4.708  24.363   1812
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 16.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.21), residues: 1690
  helix:  0.67 (0.19), residues: 708
  sheet: -0.56 (0.33), residues: 252
  loop :  0.42 (0.24), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 733 
 HIS   0.007   0.001   HIS B 785 
 PHE   0.020   0.002   PHE B 381 
 TYR   0.021   0.002   TYR A  38 
 ARG   0.010   0.001   ARG A 732 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03785 (  602)
  hydrogen bonds       : angle       5.55784 ( 1728)
  covalent geometry    : bond        0.00302 (13242)
  covalent geometry    : angle       0.64069 (17966)

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

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

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 1.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.8847 (mp10) cc_final: 0.8625 (pm20)
REVERT: A  197 MET cc_start: 0.9147 (mtp) cc_final: 0.8676 (tpp)
REVERT: A  220 LYS cc_start: 0.9623 (tptt) cc_final: 0.9342 (tppt)
REVERT: A  290 GLN cc_start: 0.8853 (mt0) cc_final: 0.8471 (mp10)
REVERT: A  294 MET cc_start: 0.9410 (mmm) cc_final: 0.9204 (mmm)
REVERT: A  360 MET cc_start: 0.9386 (tpp) cc_final: 0.8965 (tpp)
REVERT: A  470 MET cc_start: 0.8341 (pmm) cc_final: 0.7892 (pmm)
REVERT: A  495 LEU cc_start: 0.9357 (mt) cc_final: 0.9036 (mm)
REVERT: A  592 MET cc_start: 0.9515 (mmm) cc_final: 0.9114 (tpp)
REVERT: A  727 LYS cc_start: 0.7760 (mttt) cc_final: 0.7536 (mmtt)
REVERT: A  733 TRP cc_start: 0.8294 (t60) cc_final: 0.7934 (t60)
REVERT: A  767 HIS cc_start: 0.8879 (t70) cc_final: 0.8458 (t70)
REVERT: A  770 LEU cc_start: 0.8890 (mt) cc_final: 0.8587 (mt)
REVERT: A  785 HIS cc_start: 0.7192 (t-90) cc_final: 0.6972 (t-90)
REVERT: A  864 GLN cc_start: 0.8504 (tp40) cc_final: 0.8304 (tp40)
REVERT: B   99 MET cc_start: 0.8544 (tpp) cc_final: 0.8231 (tpp)
REVERT: B  108 LEU cc_start: 0.9666 (mt) cc_final: 0.9450 (mt)
REVERT: B  113 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8561 (mt-10)
REVERT: B  197 MET cc_start: 0.9093 (mmm) cc_final: 0.8653 (mmm)
REVERT: B  225 MET cc_start: 0.8406 (mmm) cc_final: 0.7947 (mmm)
REVERT: B  290 GLN cc_start: 0.8713 (mt0) cc_final: 0.8353 (mp10)
REVERT: B  303 LEU cc_start: 0.8400 (tp) cc_final: 0.7994 (tt)
REVERT: B  313 CYS cc_start: 0.7771 (m) cc_final: 0.7361 (t)
REVERT: B  360 MET cc_start: 0.9270 (mmp) cc_final: 0.8914 (mmt)
REVERT: B  470 MET cc_start: 0.7648 (mtm) cc_final: 0.7077 (pmm)
REVERT: B  573 ASN cc_start: 0.9093 (m-40) cc_final: 0.8763 (t0)
REVERT: B  577 CYS cc_start: 0.9364 (m) cc_final: 0.9116 (p)
REVERT: B  727 LYS cc_start: 0.7780 (mttt) cc_final: 0.7578 (mmtt)
REVERT: B  767 HIS cc_start: 0.8575 (t70) cc_final: 0.8140 (t70)
REVERT: B  770 LEU cc_start: 0.8919 (mt) cc_final: 0.8600 (mt)
REVERT: B  785 HIS cc_start: 0.7312 (t-90) cc_final: 0.6999 (t-90)
REVERT: B  794 ARG cc_start: 0.8996 (ptt90) cc_final: 0.8561 (ptt90)
REVERT: B  855 VAL cc_start: 0.9074 (p) cc_final: 0.8867 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 251
  average time/residue: 0.2336
  time to fit residues: 87.3001
Evaluate side-chains
  197 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 1.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   chunk 81 optimal weight:    0.0980
   chunk 103 optimal weight:    7.9990
   chunk 39 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   chunk 136 optimal weight:    0.0570
   chunk 26 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 162 optimal weight:    3.9990
   overall best weight:    1.0102

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.105553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.081775 restraints weight = 47794.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.084216 restraints weight = 35760.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.086078 restraints weight = 28386.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.8887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  13242  Z= 0.128
  Angle     :  0.649  10.622  17966  Z= 0.332
  Chirality :  0.045   0.171   1988
  Planarity :  0.005   0.044   2340
  Dihedral  :  4.581  20.074   1812
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.21), residues: 1690
  helix:  0.69 (0.19), residues: 704
  sheet: -0.57 (0.33), residues: 252
  loop :  0.60 (0.24), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 733 
 HIS   0.006   0.001   HIS B 785 
 PHE   0.023   0.002   PHE A 818 
 TYR   0.023   0.002   TYR A 518 
 ARG   0.010   0.001   ARG A 732 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03837 (  602)
  hydrogen bonds       : angle       5.54245 ( 1728)
  covalent geometry    : bond        0.00287 (13242)
  covalent geometry    : angle       0.64876 (17966)

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

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

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3380 Ramachandran restraints generated.
    1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 1.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 MET cc_start: 0.8721 (mpp) cc_final: 0.7721 (mpp)
REVERT: A   96 GLN cc_start: 0.8831 (mp10) cc_final: 0.8616 (pm20)
REVERT: A  197 MET cc_start: 0.9144 (mtp) cc_final: 0.8666 (tpp)
REVERT: A  220 LYS cc_start: 0.9630 (tptt) cc_final: 0.9352 (tppt)
REVERT: A  290 GLN cc_start: 0.8847 (mt0) cc_final: 0.8500 (mp10)
REVERT: A  360 MET cc_start: 0.9380 (tpp) cc_final: 0.8960 (tpp)
REVERT: A  470 MET cc_start: 0.8311 (pmm) cc_final: 0.7887 (pmm)
REVERT: A  592 MET cc_start: 0.9445 (mmm) cc_final: 0.9025 (tpp)
REVERT: A  733 TRP cc_start: 0.8267 (t60) cc_final: 0.7858 (t60)
REVERT: A  767 HIS cc_start: 0.8910 (t70) cc_final: 0.8502 (t70)
REVERT: A  770 LEU cc_start: 0.8987 (mt) cc_final: 0.8652 (mt)
REVERT: A  785 HIS cc_start: 0.7148 (t-90) cc_final: 0.6946 (t-90)
REVERT: A  831 LEU cc_start: 0.8336 (pp) cc_final: 0.8092 (pp)
REVERT: A  864 GLN cc_start: 0.8500 (tp40) cc_final: 0.8293 (tp40)
REVERT: B   99 MET cc_start: 0.8514 (tpp) cc_final: 0.8303 (tpp)
REVERT: B  104 THR cc_start: 0.9106 (m) cc_final: 0.8844 (p)
REVERT: B  113 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8550 (mt-10)
REVERT: B  186 VAL cc_start: 0.8965 (t) cc_final: 0.8390 (t)
REVERT: B  197 MET cc_start: 0.9100 (mmm) cc_final: 0.8653 (mmm)
REVERT: B  225 MET cc_start: 0.8417 (mmm) cc_final: 0.7941 (mmm)
REVERT: B  290 GLN cc_start: 0.8682 (mt0) cc_final: 0.8350 (mp10)
REVERT: B  313 CYS cc_start: 0.7733 (m) cc_final: 0.7352 (m)
REVERT: B  360 MET cc_start: 0.9201 (mmp) cc_final: 0.8851 (mmt)
REVERT: B  513 GLU cc_start: 0.8272 (tp30) cc_final: 0.7939 (tp30)
REVERT: B  573 ASN cc_start: 0.9093 (m-40) cc_final: 0.8765 (t0)
REVERT: B  577 CYS cc_start: 0.9361 (m) cc_final: 0.9126 (p)
REVERT: B  597 ASP cc_start: 0.9379 (m-30) cc_final: 0.9031 (t0)
REVERT: B  627 TRP cc_start: 0.8569 (m-90) cc_final: 0.8167 (m-90)
REVERT: B  649 TRP cc_start: 0.7811 (t-100) cc_final: 0.7420 (t-100)
REVERT: B  733 TRP cc_start: 0.7746 (t-100) cc_final: 0.7485 (t-100)
REVERT: B  767 HIS cc_start: 0.8547 (t70) cc_final: 0.8134 (t70)
REVERT: B  770 LEU cc_start: 0.8892 (mt) cc_final: 0.8545 (mt)
REVERT: B  785 HIS cc_start: 0.7317 (t-90) cc_final: 0.6985 (t-90)
REVERT: B  855 VAL cc_start: 0.9126 (p) cc_final: 0.8841 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 255
  average time/residue: 0.2335
  time to fit residues: 88.8066
Evaluate side-chains
  193 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 115 optimal weight:    7.9990
   chunk 162 optimal weight:    0.9980
   chunk 165 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   chunk 33 optimal weight:    0.3980
   chunk 149 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 84 optimal weight:   10.0000
   chunk 32 optimal weight:    9.9990
   chunk 152 optimal weight:    4.9990
   overall best weight:    2.8786

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.101489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.078888 restraints weight = 49796.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.081100 restraints weight = 37650.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.082778 restraints weight = 30090.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.9338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  13242  Z= 0.192
  Angle     :  0.705  13.119  17966  Z= 0.360
  Chirality :  0.046   0.158   1988
  Planarity :  0.005   0.045   2340
  Dihedral  :  4.861  19.021   1812
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 18.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.21), residues: 1690
  helix:  0.41 (0.19), residues: 718
  sheet: -0.49 (0.35), residues: 232
  loop :  0.37 (0.24), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 733 
 HIS   0.006   0.001   HIS B 785 
 PHE   0.021   0.002   PHE B 311 
 TYR   0.026   0.002   TYR A 112 
 ARG   0.011   0.001   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04165 (  602)
  hydrogen bonds       : angle       5.79892 ( 1728)
  covalent geometry    : bond        0.00415 (13242)
  covalent geometry    : angle       0.70479 (17966)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4548.18 seconds
wall clock time: 81 minutes 18.18 seconds (4878.18 seconds total)