Starting phenix.real_space_refine
on Wed Jun 11 11:48:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cq1_45806/06_2025/9cq1_45806.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cq1_45806/06_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_45806/06_2025/9cq1_45806.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cq1_45806/06_2025/9cq1_45806.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cq1_45806/06_2025/9cq1_45806.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cq1_45806/06_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): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.16, per 1000 atoms: 0.79
  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: 3.19
  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: 1.75
  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: 6.34

  Time building geometry restraints manager: 3.73 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:             82.030
  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:                     37.040
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  123.600
-------------------------------------------------------------------------------
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  : 1.548 
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: 0.3817
  time to fit residues: 235.9626
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  : 1.835 
-------------------------------------------------------------------------------
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 = 38)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.093752 restraints weight = 45047.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.096563 restraints weight = 34721.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.098683 restraints weight = 27990.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
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  : 2.033 
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: 0.9407 (mt) cc_final: 0.9195 (mt)
REVERT: A  109 GLU cc_start: 0.8650 (tt0) cc_final: 0.7622 (tt0)
REVERT: A  145 TRP cc_start: 0.7403 (m-10) cc_final: 0.7161 (m-10)
REVERT: A  197 MET cc_start: 0.8895 (mtp) cc_final: 0.8259 (mmt)
REVERT: A  220 LYS cc_start: 0.9651 (tptt) cc_final: 0.9425 (tppt)
REVERT: A  225 MET cc_start: 0.7392 (tpp) cc_final: 0.7142 (tpp)
REVERT: A  227 MET cc_start: 0.8513 (mmp) cc_final: 0.8296 (mmp)
REVERT: A  263 ILE cc_start: 0.8249 (mt) cc_final: 0.7916 (mt)
REVERT: A  270 VAL cc_start: 0.9333 (t) cc_final: 0.9009 (p)
REVERT: A  370 MET cc_start: 0.8550 (mtt) cc_final: 0.8262 (mtt)
REVERT: A  462 GLU cc_start: 0.9182 (tt0) cc_final: 0.8626 (tt0)
REVERT: A  518 TYR cc_start: 0.8552 (m-80) cc_final: 0.7997 (m-80)
REVERT: A  532 LEU cc_start: 0.9413 (mm) cc_final: 0.9086 (mt)
REVERT: A  575 PHE cc_start: 0.8752 (m-10) cc_final: 0.8502 (m-80)
REVERT: A  767 HIS cc_start: 0.8813 (t70) cc_final: 0.8520 (t70)
REVERT: A  820 SER cc_start: 0.9428 (m) cc_final: 0.9119 (p)
REVERT: B   57 MET cc_start: 0.8370 (mpp) cc_final: 0.7069 (mpp)
REVERT: B   92 LEU cc_start: 0.8578 (mt) cc_final: 0.8304 (mt)
REVERT: B  107 LEU cc_start: 0.9686 (tp) cc_final: 0.9390 (tp)
REVERT: B  155 MET cc_start: 0.7699 (mtm) cc_final: 0.7399 (mmm)
REVERT: B  197 MET cc_start: 0.8835 (mmm) cc_final: 0.8364 (mmm)
REVERT: B  263 ILE cc_start: 0.8388 (mt) cc_final: 0.8175 (mt)
REVERT: B  270 VAL cc_start: 0.9474 (t) cc_final: 0.9169 (p)
REVERT: B  294 MET cc_start: 0.8960 (mtm) cc_final: 0.8397 (mmm)
REVERT: B  333 MET cc_start: 0.7230 (mmm) cc_final: 0.6630 (mtp)
REVERT: B  532 LEU cc_start: 0.9381 (mm) cc_final: 0.9127 (mt)
REVERT: B  702 ILE cc_start: 0.9382 (mp) cc_final: 0.9048 (mp)
REVERT: B  760 LEU cc_start: 0.7833 (tp) cc_final: 0.7069 (mm)
REVERT: B  767 HIS cc_start: 0.8385 (t70) cc_final: 0.8150 (t70)
REVERT: B  770 LEU cc_start: 0.8906 (mt) cc_final: 0.8691 (mt)
REVERT: B  796 LEU cc_start: 0.8479 (mt) cc_final: 0.8032 (mt)
  outliers start: 3
  outliers final: 0
  residues processed: 314
  average time/residue: 0.2775
  time to fit residues: 125.5704
Evaluate side-chains
  214 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 20 optimal weight:    0.0770
   chunk 77 optimal weight:    8.9990
   chunk 70 optimal weight:    8.9990
   chunk 84 optimal weight:   10.0000
   chunk 48 optimal weight:    9.9990
   chunk 87 optimal weight:    6.9990
   chunk 109 optimal weight:   10.0000
   chunk 138 optimal weight:    8.9990
   chunk 51 optimal weight:    5.9990
   chunk 117 optimal weight:    0.8980
   overall best weight:    2.9742

-------------------------------------------------------------------------------
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
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 = 0.3975 r_free = 0.3975 target = 0.112070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.086831 restraints weight = 47867.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.089442 restraints weight = 36278.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.091427 restraints weight = 28630.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.5191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  13242  Z= 0.211
  Angle     :  0.673   7.740  17966  Z= 0.353
  Chirality :  0.046   0.182   1988
  Planarity :  0.005   0.050   2340
  Dihedral  :  4.827  22.565   1812
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 16.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.56 %
    Favored  : 97.30 %
  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:  0.69 (0.20), residues: 1690
  helix:  0.59 (0.19), residues: 714
  sheet:  0.12 (0.34), residues: 228
  loop :  0.69 (0.24), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP A 859 
 HIS   0.007   0.002   HIS A 423 
 PHE   0.031   0.002   PHE A 311 
 TYR   0.018   0.002   TYR A 112 
 ARG   0.007   0.001   ARG A 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04594 (  602)
  hydrogen bonds       : angle       5.78761 ( 1728)
  covalent geometry    : bond        0.00452 (13242)
  covalent geometry    : angle       0.67288 (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
  269 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 267
  time to evaluate  : 2.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: 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: 0.9502 (tp) cc_final: 0.9216 (tp)
REVERT: A  113 GLU cc_start: 0.8432 (mp0) cc_final: 0.8029 (mm-30)
REVERT: A  145 TRP cc_start: 0.7757 (m-10) cc_final: 0.7431 (m-10)
REVERT: A  197 MET cc_start: 0.9062 (mtp) cc_final: 0.8643 (mmm)
REVERT: A  220 LYS cc_start: 0.9652 (tptt) cc_final: 0.9365 (tppt)
REVERT: A  225 MET cc_start: 0.7759 (tpp) cc_final: 0.7504 (tpp)
REVERT: A  263 ILE cc_start: 0.8351 (mt) cc_final: 0.8083 (mt)
REVERT: A  294 MET cc_start: 0.9433 (mtt) cc_final: 0.8865 (mmt)
REVERT: A  360 MET cc_start: 0.9281 (tpp) cc_final: 0.8794 (tpp)
REVERT: A  518 TYR cc_start: 0.8640 (m-80) cc_final: 0.8061 (m-80)
REVERT: A  532 LEU cc_start: 0.9411 (mm) cc_final: 0.9198 (mt)
REVERT: A  579 THR cc_start: 0.9256 (p) cc_final: 0.8963 (p)
REVERT: A  582 GLN cc_start: 0.9356 (mt0) cc_final: 0.8900 (mt0)
REVERT: A  602 HIS cc_start: 0.8474 (t-90) cc_final: 0.8209 (t70)
REVERT: A  733 TRP cc_start: 0.8167 (t60) cc_final: 0.7676 (t60)
REVERT: A  767 HIS cc_start: 0.8907 (t70) cc_final: 0.8681 (t70)
REVERT: A  820 SER cc_start: 0.9419 (m) cc_final: 0.9172 (p)
REVERT: B   57 MET cc_start: 0.8614 (mpp) cc_final: 0.8178 (mpp)
REVERT: B   92 LEU cc_start: 0.8890 (mt) cc_final: 0.8652 (mt)
REVERT: B   99 MET cc_start: 0.8352 (mmp) cc_final: 0.8026 (tpp)
REVERT: B  107 LEU cc_start: 0.9675 (tp) cc_final: 0.9352 (tp)
REVERT: B  108 LEU cc_start: 0.9576 (mt) cc_final: 0.9298 (mt)
REVERT: B  111 CYS cc_start: 0.9371 (m) cc_final: 0.9156 (m)
REVERT: B  150 ASP cc_start: 0.8435 (m-30) cc_final: 0.8154 (m-30)
REVERT: B  197 MET cc_start: 0.8889 (mmm) cc_final: 0.8574 (mmm)
REVERT: B  263 ILE cc_start: 0.8396 (mt) cc_final: 0.8161 (mt)
REVERT: B  417 MET cc_start: 0.8811 (ptp) cc_final: 0.8473 (ptp)
REVERT: B  528 MET cc_start: 0.8223 (pmm) cc_final: 0.7111 (pmm)
REVERT: B  532 LEU cc_start: 0.9386 (mm) cc_final: 0.9185 (mt)
REVERT: B  577 CYS cc_start: 0.9023 (m) cc_final: 0.8551 (t)
REVERT: B  579 THR cc_start: 0.9187 (p) cc_final: 0.8851 (p)
REVERT: B  582 GLN cc_start: 0.9296 (mt0) cc_final: 0.9017 (mt0)
REVERT: B  592 MET cc_start: 0.9494 (mmp) cc_final: 0.9160 (tpp)
REVERT: B  616 LEU cc_start: 0.6734 (mp) cc_final: 0.6516 (mp)
REVERT: B  770 LEU cc_start: 0.9038 (mt) cc_final: 0.8808 (mt)
REVERT: B  844 VAL cc_start: 0.8625 (m) cc_final: 0.8335 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 268
  average time/residue: 0.2817
  time to fit residues: 114.4825
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  : 2.017 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 150 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 148 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 160 optimal weight:    8.9990
   chunk 113 optimal weight:    3.9990
   overall best weight:    0.9786

-------------------------------------------------------------------------------
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
B 195 GLN
B 350 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.114616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.088948 restraints weight = 45228.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.091613 restraints weight = 34047.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.093688 restraints weight = 27000.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.5444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13242  Z= 0.124
  Angle     :  0.586  11.290  17966  Z= 0.297
  Chirality :  0.044   0.162   1988
  Planarity :  0.004   0.043   2340
  Dihedral  :  4.400  15.104   1812
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.85 %
    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:  0.93 (0.20), residues: 1690
  helix:  1.01 (0.19), residues: 712
  sheet: -0.08 (0.33), residues: 242
  loop :  0.70 (0.24), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 859 
 HIS   0.005   0.001   HIS A 371 
 PHE   0.027   0.002   PHE A 818 
 TYR   0.018   0.001   TYR A 704 
 ARG   0.010   0.000   ARG B 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03863 (  602)
  hydrogen bonds       : angle       5.38714 ( 1728)
  covalent geometry    : bond        0.00283 (13242)
  covalent geometry    : angle       0.58641 (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
  266 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 265
  time to evaluate  : 1.666 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 MET cc_start: 0.8683 (mpp) cc_final: 0.8141 (mpp)
REVERT: A   92 LEU cc_start: 0.8838 (mt) cc_final: 0.8606 (mt)
REVERT: A   96 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8688 (mp10)
REVERT: A   99 MET cc_start: 0.8391 (mmt) cc_final: 0.7907 (mmm)
REVERT: A  104 THR cc_start: 0.9273 (m) cc_final: 0.8975 (p)
REVERT: A  108 LEU cc_start: 0.9515 (mt) cc_final: 0.9243 (mt)
REVERT: A  197 MET cc_start: 0.9052 (mtp) cc_final: 0.8645 (mmm)
REVERT: A  220 LYS cc_start: 0.9661 (tptt) cc_final: 0.9371 (tppt)
REVERT: A  294 MET cc_start: 0.9476 (mtt) cc_final: 0.9149 (mmm)
REVERT: A  333 MET cc_start: 0.7178 (mtp) cc_final: 0.6740 (mtp)
REVERT: A  360 MET cc_start: 0.9311 (tpp) cc_final: 0.9063 (tpp)
REVERT: A  370 MET cc_start: 0.8873 (mtt) cc_final: 0.8453 (mtt)
REVERT: A  447 THR cc_start: 0.8383 (p) cc_final: 0.8097 (p)
REVERT: A  533 MET cc_start: 0.8380 (tpt) cc_final: 0.8167 (tpp)
REVERT: A  581 ILE cc_start: 0.9393 (mt) cc_final: 0.9180 (mt)
REVERT: A  592 MET cc_start: 0.9596 (mmm) cc_final: 0.9215 (mmm)
REVERT: A  609 CYS cc_start: 0.8118 (m) cc_final: 0.7584 (m)
REVERT: A  733 TRP cc_start: 0.8022 (t60) cc_final: 0.7548 (t60)
REVERT: A  767 HIS cc_start: 0.8922 (t70) cc_final: 0.8672 (t-170)
REVERT: A  820 SER cc_start: 0.9437 (m) cc_final: 0.9198 (p)
REVERT: B   57 MET cc_start: 0.8633 (mpp) cc_final: 0.7669 (mpp)
REVERT: B   92 LEU cc_start: 0.8960 (mt) cc_final: 0.8739 (mt)
REVERT: B   99 MET cc_start: 0.8466 (mmp) cc_final: 0.8217 (tpp)
REVERT: B  107 LEU cc_start: 0.9651 (tp) cc_final: 0.9361 (tp)
REVERT: B  108 LEU cc_start: 0.9575 (mt) cc_final: 0.9274 (mt)
REVERT: B  113 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8148 (mt-10)
REVERT: B  150 ASP cc_start: 0.8364 (m-30) cc_final: 0.8132 (m-30)
REVERT: B  187 LEU cc_start: 0.9611 (mm) cc_final: 0.9346 (tp)
REVERT: B  197 MET cc_start: 0.8974 (mmm) cc_final: 0.8618 (mmm)
REVERT: B  294 MET cc_start: 0.9450 (mtt) cc_final: 0.8852 (mmm)
REVERT: B  333 MET cc_start: 0.6954 (mtp) cc_final: 0.6210 (mtp)
REVERT: B  360 MET cc_start: 0.9506 (mmm) cc_final: 0.9043 (tpp)
REVERT: B  417 MET cc_start: 0.8788 (ptp) cc_final: 0.8502 (ptp)
REVERT: B  484 LEU cc_start: 0.8388 (tt) cc_final: 0.8060 (tp)
REVERT: B  577 CYS cc_start: 0.9053 (m) cc_final: 0.8635 (t)
REVERT: B  579 THR cc_start: 0.9263 (p) cc_final: 0.8950 (p)
REVERT: B  581 ILE cc_start: 0.9260 (mt) cc_final: 0.8995 (mt)
REVERT: B  582 GLN cc_start: 0.9381 (mt0) cc_final: 0.8979 (mt0)
REVERT: B  592 MET cc_start: 0.9458 (mmp) cc_final: 0.9203 (tpp)
REVERT: B  616 LEU cc_start: 0.6683 (mp) cc_final: 0.6468 (mp)
REVERT: B  673 ILE cc_start: 0.8629 (pt) cc_final: 0.8399 (pt)
REVERT: B  709 MET cc_start: 0.8653 (mmt) cc_final: 0.8325 (mmt)
REVERT: B  733 TRP cc_start: 0.8109 (t60) cc_final: 0.7808 (t60)
REVERT: B  767 HIS cc_start: 0.8416 (t70) cc_final: 0.8072 (t70)
REVERT: B  770 LEU cc_start: 0.8874 (mt) cc_final: 0.8664 (mt)
REVERT: B  855 VAL cc_start: 0.9078 (p) cc_final: 0.8707 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 266
  average time/residue: 0.2935
  time to fit residues: 116.8305
Evaluate side-chains
  195 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 3.184 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 10 optimal weight:    9.9990
   chunk 123 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 98 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   chunk 151 optimal weight:   20.0000
   chunk 40 optimal weight:    0.9980
   chunk 150 optimal weight:    1.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 HIS
B 350 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 655 GLN
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 = 0.3975 r_free = 0.3975 target = 0.110861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.086233 restraints weight = 46288.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.088796 restraints weight = 34702.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.090736 restraints weight = 27474.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.6121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  13242  Z= 0.154
  Angle     :  0.623  10.526  17966  Z= 0.315
  Chirality :  0.045   0.179   1988
  Planarity :  0.005   0.088   2340
  Dihedral  :  4.412  17.293   1812
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 15.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    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:  0.79 (0.20), residues: 1690
  helix:  0.89 (0.19), residues: 708
  sheet: -0.24 (0.32), residues: 264
  loop :  0.69 (0.24), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 627 
 HIS   0.004   0.001   HIS B 785 
 PHE   0.021   0.002   PHE A 818 
 TYR   0.016   0.002   TYR B 112 
 ARG   0.011   0.001   ARG B 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03997 (  602)
  hydrogen bonds       : angle       5.46022 ( 1728)
  covalent geometry    : bond        0.00351 (13242)
  covalent geometry    : angle       0.62302 (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
  256 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 1.293 
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: 0.8677 (mpp) cc_final: 0.8085 (mpp)
REVERT: A   92 LEU cc_start: 0.8916 (mt) cc_final: 0.8615 (mt)
REVERT: A   99 MET cc_start: 0.8384 (mmt) cc_final: 0.8130 (mmm)
REVERT: A  104 THR cc_start: 0.9300 (m) cc_final: 0.9001 (p)
REVERT: A  108 LEU cc_start: 0.9516 (mt) cc_final: 0.9235 (mt)
REVERT: A  145 TRP cc_start: 0.7451 (m-10) cc_final: 0.7244 (m-10)
REVERT: A  197 MET cc_start: 0.9068 (mtp) cc_final: 0.8805 (mmm)
REVERT: A  220 LYS cc_start: 0.9643 (tptt) cc_final: 0.9334 (tppt)
REVERT: A  263 ILE cc_start: 0.8334 (mt) cc_final: 0.8132 (mt)
REVERT: A  294 MET cc_start: 0.9510 (mtt) cc_final: 0.9275 (mmm)
REVERT: A  333 MET cc_start: 0.7408 (mtp) cc_final: 0.7030 (mtp)
REVERT: A  360 MET cc_start: 0.9424 (tpp) cc_final: 0.9070 (tpp)
REVERT: A  370 MET cc_start: 0.9069 (mtt) cc_final: 0.8801 (mtt)
REVERT: A  410 MET cc_start: 0.8794 (mmt) cc_final: 0.8565 (mmt)
REVERT: A  533 MET cc_start: 0.8478 (tpt) cc_final: 0.8264 (tpp)
REVERT: A  592 MET cc_start: 0.9614 (mmm) cc_final: 0.9153 (mmm)
REVERT: A  616 LEU cc_start: 0.6685 (mp) cc_final: 0.6474 (mp)
REVERT: A  767 HIS cc_start: 0.8882 (t70) cc_final: 0.8421 (t70)
REVERT: A  770 LEU cc_start: 0.8770 (mt) cc_final: 0.8517 (mt)
REVERT: A  820 SER cc_start: 0.9398 (m) cc_final: 0.9184 (p)
REVERT: B   92 LEU cc_start: 0.8969 (mt) cc_final: 0.8742 (mt)
REVERT: B  113 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8240 (mt-10)
REVERT: B  150 ASP cc_start: 0.8440 (m-30) cc_final: 0.7879 (m-30)
REVERT: B  187 LEU cc_start: 0.9660 (mm) cc_final: 0.9363 (tp)
REVERT: B  197 MET cc_start: 0.8933 (mmm) cc_final: 0.8568 (mmm)
REVERT: B  220 LYS cc_start: 0.9429 (mmmt) cc_final: 0.9024 (mmmt)
REVERT: B  294 MET cc_start: 0.9472 (mtt) cc_final: 0.9246 (mmm)
REVERT: B  333 MET cc_start: 0.7357 (mtp) cc_final: 0.6831 (mtp)
REVERT: B  360 MET cc_start: 0.9531 (mmm) cc_final: 0.8796 (tpt)
REVERT: B  417 MET cc_start: 0.8792 (ptp) cc_final: 0.8458 (ptp)
REVERT: B  449 SER cc_start: 0.7940 (m) cc_final: 0.7621 (p)
REVERT: B  484 LEU cc_start: 0.8442 (tt) cc_final: 0.7870 (tp)
REVERT: B  528 MET cc_start: 0.8220 (pmm) cc_final: 0.7879 (pmm)
REVERT: B  577 CYS cc_start: 0.9100 (m) cc_final: 0.8658 (t)
REVERT: B  592 MET cc_start: 0.9431 (mmp) cc_final: 0.9194 (tpp)
REVERT: B  609 CYS cc_start: 0.8820 (m) cc_final: 0.8581 (m)
REVERT: B  616 LEU cc_start: 0.6567 (mp) cc_final: 0.6336 (mp)
REVERT: B  733 TRP cc_start: 0.8148 (t60) cc_final: 0.7831 (t60)
REVERT: B  767 HIS cc_start: 0.8510 (t70) cc_final: 0.8107 (t70)
REVERT: B  770 LEU cc_start: 0.8950 (mt) cc_final: 0.8738 (mt)
REVERT: B  855 VAL cc_start: 0.9120 (p) cc_final: 0.8818 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 256
  average time/residue: 0.3312
  time to fit residues: 128.9418
Evaluate side-chains
  187 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 3.344 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 151 optimal weight:    9.9990
   chunk 104 optimal weight:    0.9980
   chunk 77 optimal weight:    0.0970
   chunk 132 optimal weight:    7.9990
   chunk 96 optimal weight:    0.4980
   chunk 95 optimal weight:    7.9990
   chunk 20 optimal weight:   10.0000
   chunk 133 optimal weight:    0.7980
   chunk 159 optimal weight:    4.9990
   overall best weight:    1.4780

-------------------------------------------------------------------------------
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 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 655 GLN
A 705 HIS
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.111007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.085966 restraints weight = 46720.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.088638 restraints weight = 35007.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.090689 restraints weight = 27566.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.6580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13242  Z= 0.138
  Angle     :  0.610   9.655  17966  Z= 0.307
  Chirality :  0.045   0.171   1988
  Planarity :  0.004   0.038   2340
  Dihedral  :  4.440  18.928   1812
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  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:  0.76 (0.21), residues: 1690
  helix:  0.94 (0.19), residues: 722
  sheet: -0.35 (0.33), residues: 252
  loop :  0.59 (0.24), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 145 
 HIS   0.005   0.001   HIS B 785 
 PHE   0.015   0.002   PHE A 818 
 TYR   0.015   0.001   TYR A  38 
 ARG   0.004   0.000   ARG B  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03729 (  602)
  hydrogen bonds       : angle       5.41237 ( 1728)
  covalent geometry    : bond        0.00312 (13242)
  covalent geometry    : angle       0.60981 (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
  249 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 3.014 
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: 0.8811 (mpp) cc_final: 0.8092 (mpp)
REVERT: A   92 LEU cc_start: 0.9080 (mt) cc_final: 0.8749 (mt)
REVERT: A   96 GLN cc_start: 0.9036 (mp10) cc_final: 0.8723 (mp10)
REVERT: A  104 THR cc_start: 0.9306 (m) cc_final: 0.9012 (p)
REVERT: A  108 LEU cc_start: 0.9530 (mt) cc_final: 0.9249 (mt)
REVERT: A  197 MET cc_start: 0.9167 (mtp) cc_final: 0.8872 (mmm)
REVERT: A  220 LYS cc_start: 0.9647 (tptt) cc_final: 0.9352 (tppt)
REVERT: A  294 MET cc_start: 0.9556 (mtt) cc_final: 0.9274 (mmm)
REVERT: A  333 MET cc_start: 0.7736 (mtp) cc_final: 0.7479 (mtp)
REVERT: A  360 MET cc_start: 0.9488 (tpp) cc_final: 0.9275 (tpp)
REVERT: A  533 MET cc_start: 0.8434 (tpt) cc_final: 0.8169 (tpp)
REVERT: A  582 GLN cc_start: 0.9664 (tt0) cc_final: 0.9259 (tp40)
REVERT: A  592 MET cc_start: 0.9620 (mmm) cc_final: 0.9212 (mmm)
REVERT: A  733 TRP cc_start: 0.8447 (t60) cc_final: 0.8112 (t60)
REVERT: A  767 HIS cc_start: 0.8967 (t70) cc_final: 0.8522 (t70)
REVERT: A  770 LEU cc_start: 0.8764 (mt) cc_final: 0.8471 (mt)
REVERT: A  820 SER cc_start: 0.9404 (m) cc_final: 0.9197 (p)
REVERT: B   96 GLN cc_start: 0.8853 (mp10) cc_final: 0.8496 (mp10)
REVERT: B  113 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8416 (mt-10)
REVERT: B  190 LEU cc_start: 0.9691 (tp) cc_final: 0.9451 (tt)
REVERT: B  197 MET cc_start: 0.9016 (mmm) cc_final: 0.8638 (mmm)
REVERT: B  333 MET cc_start: 0.7585 (mtp) cc_final: 0.7078 (mtp)
REVERT: B  360 MET cc_start: 0.9563 (mmm) cc_final: 0.8820 (tpt)
REVERT: B  410 MET cc_start: 0.8973 (mtt) cc_final: 0.8753 (mtm)
REVERT: B  462 GLU cc_start: 0.9223 (tt0) cc_final: 0.9015 (tp30)
REVERT: B  484 LEU cc_start: 0.8507 (tt) cc_final: 0.8060 (tp)
REVERT: B  487 MET cc_start: 0.9216 (tpp) cc_final: 0.8864 (tpp)
REVERT: B  582 GLN cc_start: 0.9607 (tt0) cc_final: 0.9246 (tp40)
REVERT: B  592 MET cc_start: 0.9492 (mmp) cc_final: 0.9223 (tpp)
REVERT: B  604 MET cc_start: 0.8655 (mpp) cc_final: 0.8441 (mpp)
REVERT: B  616 LEU cc_start: 0.6576 (mp) cc_final: 0.6343 (mp)
REVERT: B  733 TRP cc_start: 0.8039 (t60) cc_final: 0.7617 (t60)
REVERT: B  767 HIS cc_start: 0.8573 (t70) cc_final: 0.8165 (t70)
REVERT: B  770 LEU cc_start: 0.8966 (mt) cc_final: 0.8637 (mt)
REVERT: B  785 HIS cc_start: 0.7458 (t-90) cc_final: 0.7224 (t-90)
REVERT: B  855 VAL cc_start: 0.9077 (p) cc_final: 0.8367 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.3612
  time to fit residues: 140.7337
Evaluate side-chains
  186 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 1.781 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 103 optimal weight:    3.9990
   chunk 85 optimal weight:    7.9990
   chunk 32 optimal weight:    9.9990
   chunk 91 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 28 optimal weight:    7.9990
   chunk 50 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 24 optimal weight:    9.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
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 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 HIS
B 149 GLN
B 378 ASN
** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.109826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.085579 restraints weight = 46749.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.088148 restraints weight = 35027.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.090123 restraints weight = 27761.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.7000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13242  Z= 0.138
  Angle     :  0.617   9.707  17966  Z= 0.310
  Chirality :  0.045   0.156   1988
  Planarity :  0.004   0.037   2340
  Dihedral  :  4.430  21.795   1812
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  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:  0.76 (0.21), residues: 1690
  helix:  0.95 (0.20), residues: 726
  sheet: -0.31 (0.33), residues: 256
  loop :  0.59 (0.24), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B 627 
 HIS   0.006   0.001   HIS B 785 
 PHE   0.021   0.002   PHE A 311 
 TYR   0.021   0.001   TYR A  38 
 ARG   0.003   0.000   ARG A 732 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03697 (  602)
  hydrogen bonds       : angle       5.33722 ( 1728)
  covalent geometry    : bond        0.00308 (13242)
  covalent geometry    : angle       0.61714 (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
  245 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 1.302 
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: 0.9066 (mt) cc_final: 0.8764 (mt)
REVERT: A   96 GLN cc_start: 0.9057 (mp10) cc_final: 0.8777 (mp10)
REVERT: A  104 THR cc_start: 0.9295 (m) cc_final: 0.9017 (p)
REVERT: A  108 LEU cc_start: 0.9533 (mt) cc_final: 0.9287 (mt)
REVERT: A  197 MET cc_start: 0.9135 (mtp) cc_final: 0.8851 (mmm)
REVERT: A  220 LYS cc_start: 0.9627 (tptt) cc_final: 0.9055 (tppt)
REVERT: A  462 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8400 (tm-30)
REVERT: A  470 MET cc_start: 0.8382 (pmm) cc_final: 0.7979 (pmm)
REVERT: A  533 MET cc_start: 0.8494 (tpt) cc_final: 0.8260 (tpp)
REVERT: A  582 GLN cc_start: 0.9657 (tt0) cc_final: 0.9144 (tp-100)
REVERT: A  592 MET cc_start: 0.9568 (mmm) cc_final: 0.9066 (tmm)
REVERT: A  733 TRP cc_start: 0.8249 (t60) cc_final: 0.7903 (t60)
REVERT: A  767 HIS cc_start: 0.8939 (t70) cc_final: 0.8489 (t70)
REVERT: A  770 LEU cc_start: 0.8855 (mt) cc_final: 0.8560 (mt)
REVERT: A  844 VAL cc_start: 0.8811 (m) cc_final: 0.8573 (p)
REVERT: B  108 LEU cc_start: 0.9629 (mt) cc_final: 0.9415 (mt)
REVERT: B  113 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8350 (mt-10)
REVERT: B  187 LEU cc_start: 0.9639 (mm) cc_final: 0.9422 (tp)
REVERT: B  190 LEU cc_start: 0.9721 (tp) cc_final: 0.9470 (tt)
REVERT: B  197 MET cc_start: 0.9003 (mmm) cc_final: 0.8621 (mmm)
REVERT: B  294 MET cc_start: 0.9363 (mmm) cc_final: 0.8360 (mmm)
REVERT: B  333 MET cc_start: 0.7568 (mtp) cc_final: 0.7246 (mtp)
REVERT: B  360 MET cc_start: 0.9482 (mmm) cc_final: 0.8991 (tpt)
REVERT: B  448 TYR cc_start: 0.9241 (t80) cc_final: 0.8634 (t80)
REVERT: B  476 CYS cc_start: 0.9199 (m) cc_final: 0.8992 (m)
REVERT: B  582 GLN cc_start: 0.9578 (tt0) cc_final: 0.8902 (tp40)
REVERT: B  592 MET cc_start: 0.9479 (mmp) cc_final: 0.9213 (tpp)
REVERT: B  616 LEU cc_start: 0.6617 (mp) cc_final: 0.6410 (mp)
REVERT: B  733 TRP cc_start: 0.8034 (t60) cc_final: 0.7685 (t60)
REVERT: B  767 HIS cc_start: 0.8543 (t70) cc_final: 0.8114 (t70)
REVERT: B  770 LEU cc_start: 0.8945 (mt) cc_final: 0.8616 (mt)
REVERT: B  855 VAL cc_start: 0.8810 (p) cc_final: 0.8423 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 245
  average time/residue: 0.2518
  time to fit residues: 92.1369
Evaluate side-chains
  183 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.514 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 145 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 57 optimal weight:    8.9990
   chunk 59 optimal weight:    9.9990
   chunk 63 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 117 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 314 HIS
A 350 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 HIS
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 582 GLN ** 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 = 0.3929 r_free = 0.3929 target = 0.107626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.083427 restraints weight = 48641.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.085960 restraints weight = 36348.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.087914 restraints weight = 28694.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.7491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13242  Z= 0.145
  Angle     :  0.615   9.151  17966  Z= 0.309
  Chirality :  0.045   0.165   1988
  Planarity :  0.005   0.045   2340
  Dihedral  :  4.472  20.246   1812
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 15.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  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:  0.75 (0.21), residues: 1690
  helix:  0.98 (0.19), residues: 724
  sheet: -0.43 (0.32), residues: 258
  loop :  0.58 (0.24), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 145 
 HIS   0.005   0.001   HIS B 437 
 PHE   0.011   0.002   PHE A 311 
 TYR   0.021   0.002   TYR A  38 
 ARG   0.011   0.001   ARG A 732 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03631 (  602)
  hydrogen bonds       : angle       5.43459 ( 1728)
  covalent geometry    : bond        0.00319 (13242)
  covalent geometry    : angle       0.61536 (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
  238 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 1.429 
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   92 LEU cc_start: 0.9123 (mt) cc_final: 0.8822 (mt)
REVERT: A   96 GLN cc_start: 0.9098 (mp10) cc_final: 0.8841 (mp10)
REVERT: A  104 THR cc_start: 0.9312 (m) cc_final: 0.9050 (p)
REVERT: A  108 LEU cc_start: 0.9562 (mt) cc_final: 0.9303 (mt)
REVERT: A  197 MET cc_start: 0.9155 (mtp) cc_final: 0.8849 (mmm)
REVERT: A  220 LYS cc_start: 0.9622 (tptt) cc_final: 0.9379 (tppt)
REVERT: A  290 GLN cc_start: 0.8804 (mt0) cc_final: 0.8354 (mp10)
REVERT: A  360 MET cc_start: 0.9358 (tpp) cc_final: 0.9011 (ttm)
REVERT: A  406 SER cc_start: 0.8402 (p) cc_final: 0.7930 (t)
REVERT: A  462 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8434 (tm-30)
REVERT: A  470 MET cc_start: 0.8398 (pmm) cc_final: 0.7987 (pmm)
REVERT: A  533 MET cc_start: 0.8604 (tpt) cc_final: 0.8377 (tpp)
REVERT: A  582 GLN cc_start: 0.9662 (tt0) cc_final: 0.9189 (tp-100)
REVERT: A  592 MET cc_start: 0.9538 (mmm) cc_final: 0.8516 (tpp)
REVERT: A  733 TRP cc_start: 0.8371 (t60) cc_final: 0.8008 (t60)
REVERT: A  767 HIS cc_start: 0.8945 (t70) cc_final: 0.8526 (t-170)
REVERT: A  770 LEU cc_start: 0.8882 (mt) cc_final: 0.8571 (mt)
REVERT: A  844 VAL cc_start: 0.8885 (m) cc_final: 0.8656 (p)
REVERT: B  108 LEU cc_start: 0.9647 (mt) cc_final: 0.9439 (mt)
REVERT: B  187 LEU cc_start: 0.9667 (mm) cc_final: 0.9393 (tp)
REVERT: B  197 MET cc_start: 0.8980 (mmm) cc_final: 0.8611 (mmm)
REVERT: B  290 GLN cc_start: 0.8668 (mt0) cc_final: 0.8447 (mp10)
REVERT: B  294 MET cc_start: 0.9349 (mmm) cc_final: 0.8412 (mmm)
REVERT: B  333 MET cc_start: 0.7814 (mtp) cc_final: 0.7552 (mtp)
REVERT: B  360 MET cc_start: 0.9472 (mmm) cc_final: 0.9183 (tpp)
REVERT: B  417 MET cc_start: 0.8588 (ptp) cc_final: 0.8375 (pmm)
REVERT: B  448 TYR cc_start: 0.9276 (t80) cc_final: 0.8708 (t80)
REVERT: B  470 MET cc_start: 0.8214 (pmm) cc_final: 0.7844 (pmm)
REVERT: B  476 CYS cc_start: 0.9243 (m) cc_final: 0.9020 (m)
REVERT: B  582 GLN cc_start: 0.9602 (tt0) cc_final: 0.9091 (tp40)
REVERT: B  592 MET cc_start: 0.9500 (mmp) cc_final: 0.9216 (tpp)
REVERT: B  604 MET cc_start: 0.8550 (mpp) cc_final: 0.8313 (mpp)
REVERT: B  616 LEU cc_start: 0.6673 (mp) cc_final: 0.6451 (mp)
REVERT: B  733 TRP cc_start: 0.8070 (t60) cc_final: 0.7700 (t60)
REVERT: B  767 HIS cc_start: 0.8526 (t70) cc_final: 0.8193 (t70)
REVERT: B  770 LEU cc_start: 0.8983 (mt) cc_final: 0.8668 (mt)
REVERT: B  785 HIS cc_start: 0.7499 (t-90) cc_final: 0.7117 (t-90)
REVERT: B  844 VAL cc_start: 0.8829 (m) cc_final: 0.8600 (p)
REVERT: B  854 MET cc_start: 0.9136 (ptp) cc_final: 0.8887 (ptp)
REVERT: B  855 VAL cc_start: 0.8815 (p) cc_final: 0.8515 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.2274
  time to fit residues: 81.7835
Evaluate side-chains
  185 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 1.568 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 144 optimal weight:   10.0000
   chunk 64 optimal weight:    0.6980
   chunk 10 optimal weight:   10.0000
   chunk 100 optimal weight:    5.9990
   chunk 65 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 104 optimal weight:    3.9990
   chunk 105 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 314 HIS
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 HIS
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 582 GLN
** 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 = 0.3960 r_free = 0.3960 target = 0.109870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.085413 restraints weight = 47310.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.088014 restraints weight = 35455.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.089915 restraints weight = 28017.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.7681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13242  Z= 0.116
  Angle     :  0.599  10.478  17966  Z= 0.298
  Chirality :  0.045   0.218   1988
  Planarity :  0.004   0.038   2340
  Dihedral  :  4.345  24.500   1812
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.50 %
    Favored  : 99.43 %
  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:  0.86 (0.21), residues: 1690
  helix:  1.07 (0.20), residues: 726
  sheet: -0.38 (0.33), residues: 256
  loop :  0.65 (0.24), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 145 
 HIS   0.006   0.001   HIS B 785 
 PHE   0.016   0.002   PHE A 381 
 TYR   0.021   0.001   TYR A  38 
 ARG   0.005   0.000   ARG B  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03490 (  602)
  hydrogen bonds       : angle       5.21931 ( 1728)
  covalent geometry    : bond        0.00263 (13242)
  covalent geometry    : angle       0.59858 (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
  247 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 246
  time to evaluate  : 1.561 
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: A   92 LEU cc_start: 0.9111 (mt) cc_final: 0.8821 (mt)
REVERT: A   96 GLN cc_start: 0.9054 (mp10) cc_final: 0.8780 (mp10)
REVERT: A  104 THR cc_start: 0.9290 (m) cc_final: 0.9049 (p)
REVERT: A  108 LEU cc_start: 0.9559 (mt) cc_final: 0.9303 (mt)
REVERT: A  197 MET cc_start: 0.9102 (mtp) cc_final: 0.8864 (mmm)
REVERT: A  220 LYS cc_start: 0.9623 (tptt) cc_final: 0.9421 (tppt)
REVERT: A  290 GLN cc_start: 0.8753 (mt0) cc_final: 0.8325 (mp10)
REVERT: A  294 MET cc_start: 0.9305 (mmm) cc_final: 0.8177 (mmm)
REVERT: A  333 MET cc_start: 0.7809 (mtp) cc_final: 0.7587 (mtp)
REVERT: A  406 SER cc_start: 0.8498 (p) cc_final: 0.8147 (t)
REVERT: A  462 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8379 (tm-30)
REVERT: A  470 MET cc_start: 0.8390 (pmm) cc_final: 0.7921 (pmm)
REVERT: A  533 MET cc_start: 0.8586 (tpt) cc_final: 0.8363 (tpp)
REVERT: A  582 GLN cc_start: 0.9641 (tt0) cc_final: 0.9139 (tp-100)
REVERT: A  592 MET cc_start: 0.9413 (mmm) cc_final: 0.8672 (tpp)
REVERT: A  767 HIS cc_start: 0.8983 (t70) cc_final: 0.8555 (t-170)
REVERT: A  770 LEU cc_start: 0.8853 (mt) cc_final: 0.8530 (mt)
REVERT: A  831 LEU cc_start: 0.7997 (pp) cc_final: 0.7670 (pp)
REVERT: B  187 LEU cc_start: 0.9628 (mm) cc_final: 0.9367 (tp)
REVERT: B  197 MET cc_start: 0.8994 (mmm) cc_final: 0.8621 (mmm)
REVERT: B  225 MET cc_start: 0.8240 (mmm) cc_final: 0.7646 (mmp)
REVERT: B  290 GLN cc_start: 0.8623 (mt0) cc_final: 0.8223 (mp10)
REVERT: B  294 MET cc_start: 0.9357 (mmm) cc_final: 0.8477 (mmm)
REVERT: B  360 MET cc_start: 0.9460 (mmm) cc_final: 0.9240 (tpp)
REVERT: B  406 SER cc_start: 0.8153 (p) cc_final: 0.7663 (t)
REVERT: B  470 MET cc_start: 0.8187 (pmm) cc_final: 0.7760 (pmm)
REVERT: B  487 MET cc_start: 0.8980 (tpt) cc_final: 0.8755 (tpp)
REVERT: B  582 GLN cc_start: 0.9604 (OUTLIER) cc_final: 0.8904 (tp40)
REVERT: B  733 TRP cc_start: 0.8071 (t60) cc_final: 0.7747 (t60)
REVERT: B  767 HIS cc_start: 0.8570 (t70) cc_final: 0.8179 (t70)
REVERT: B  770 LEU cc_start: 0.8941 (mt) cc_final: 0.8589 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 246
  average time/residue: 0.2372
  time to fit residues: 86.6418
Evaluate side-chains
  190 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 189
  time to evaluate  : 1.390 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 49 optimal weight:    8.9990
   chunk 81 optimal weight:    3.9990
   chunk 103 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 87 optimal weight:    4.9990
   chunk 136 optimal weight:    0.0770
   chunk 26 optimal weight:    7.9990
   chunk 78 optimal weight:    1.9990
   chunk 162 optimal weight:    0.3980
   overall best weight:    2.2944

-------------------------------------------------------------------------------
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 705 HIS
A 756 HIS
** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 861 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.106857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.082980 restraints weight = 48416.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.085459 restraints weight = 36485.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.087307 restraints weight = 28753.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.8138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13242  Z= 0.170
  Angle     :  0.667  14.190  17966  Z= 0.338
  Chirality :  0.045   0.164   1988
  Planarity :  0.005   0.039   2340
  Dihedral  :  4.557  22.851   1812
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  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:  0.76 (0.21), residues: 1690
  helix:  0.97 (0.19), residues: 726
  sheet: -0.49 (0.32), residues: 258
  loop :  0.65 (0.25), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 515 
 HIS   0.006   0.001   HIS B 785 
 PHE   0.015   0.002   PHE B 381 
 TYR   0.021   0.002   TYR A  38 
 ARG   0.004   0.001   ARG B 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03798 (  602)
  hydrogen bonds       : angle       5.50020 ( 1728)
  covalent geometry    : bond        0.00367 (13242)
  covalent geometry    : angle       0.66728 (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
  237 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 1.545 
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   99 MET cc_start: 0.8360 (tpp) cc_final: 0.8121 (tpp)
REVERT: A  104 THR cc_start: 0.9325 (m) cc_final: 0.9113 (p)
REVERT: A  108 LEU cc_start: 0.9545 (mt) cc_final: 0.9289 (mt)
REVERT: A  197 MET cc_start: 0.9134 (mtp) cc_final: 0.8846 (tpp)
REVERT: A  220 LYS cc_start: 0.9623 (tptt) cc_final: 0.9381 (tppt)
REVERT: A  290 GLN cc_start: 0.8854 (mt0) cc_final: 0.8406 (mp10)
REVERT: A  360 MET cc_start: 0.9373 (tpp) cc_final: 0.8747 (tpp)
REVERT: A  406 SER cc_start: 0.8429 (p) cc_final: 0.8011 (t)
REVERT: A  462 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8453 (tm-30)
REVERT: A  470 MET cc_start: 0.8371 (pmm) cc_final: 0.7907 (pmm)
REVERT: A  495 LEU cc_start: 0.9214 (mt) cc_final: 0.8864 (mm)
REVERT: A  533 MET cc_start: 0.8711 (tpt) cc_final: 0.8481 (tpp)
REVERT: A  575 PHE cc_start: 0.9253 (m-80) cc_final: 0.8969 (m-80)
REVERT: A  582 GLN cc_start: 0.9658 (tt0) cc_final: 0.9165 (tp-100)
REVERT: A  592 MET cc_start: 0.9378 (mmm) cc_final: 0.8741 (tpp)
REVERT: A  733 TRP cc_start: 0.8393 (t60) cc_final: 0.8189 (t60)
REVERT: A  767 HIS cc_start: 0.8920 (t70) cc_final: 0.8472 (t-170)
REVERT: A  770 LEU cc_start: 0.8928 (mt) cc_final: 0.8609 (mt)
REVERT: B  187 LEU cc_start: 0.9640 (mm) cc_final: 0.9384 (tp)
REVERT: B  197 MET cc_start: 0.8999 (mmm) cc_final: 0.8657 (mmm)
REVERT: B  290 GLN cc_start: 0.8736 (mt0) cc_final: 0.8310 (mp10)
REVERT: B  294 MET cc_start: 0.9363 (mmm) cc_final: 0.8490 (mmm)
REVERT: B  333 MET cc_start: 0.7997 (mtp) cc_final: 0.7753 (mtp)
REVERT: B  360 MET cc_start: 0.9451 (mmm) cc_final: 0.9249 (tpp)
REVERT: B  462 GLU cc_start: 0.8781 (tp30) cc_final: 0.8423 (tp30)
REVERT: B  470 MET cc_start: 0.8290 (pmm) cc_final: 0.7861 (pmm)
REVERT: B  733 TRP cc_start: 0.8166 (t60) cc_final: 0.7826 (t60)
REVERT: B  767 HIS cc_start: 0.8557 (t70) cc_final: 0.8205 (t70)
REVERT: B  770 LEU cc_start: 0.9003 (mt) cc_final: 0.8674 (mt)
REVERT: B  785 HIS cc_start: 0.7578 (t-90) cc_final: 0.7174 (t-90)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.2202
  time to fit residues: 79.4469
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  : 1.520 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 162 optimal weight:    0.9980
   chunk 165 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 149 optimal weight:    0.5980
   chunk 42 optimal weight:    6.9990
   chunk 66 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 152 optimal weight:    7.9990
   overall best weight:    3.1186

-------------------------------------------------------------------------------
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 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 HIS
A 861 HIS
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.101822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.079156 restraints weight = 49528.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.081488 restraints weight = 37019.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.083231 restraints weight = 29170.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.9023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  13242  Z= 0.210
  Angle     :  0.717  11.465  17966  Z= 0.369
  Chirality :  0.046   0.171   1988
  Planarity :  0.005   0.051   2340
  Dihedral  :  5.036  20.488   1812
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 20.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  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:  0.46 (0.21), residues: 1690
  helix:  0.66 (0.19), residues: 720
  sheet: -0.12 (0.35), residues: 216
  loop :  0.29 (0.24), residues: 754

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP A 145 
 HIS   0.008   0.002   HIS B 785 
 PHE   0.017   0.002   PHE A 311 
 TYR   0.024   0.002   TYR A  38 
 ARG   0.011   0.001   ARG B 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04234 (  602)
  hydrogen bonds       : angle       5.93793 ( 1728)
  covalent geometry    : bond        0.00446 (13242)
  covalent geometry    : angle       0.71735 (17966)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5326.74 seconds
wall clock time: 97 minutes 50.24 seconds (5870.24 seconds total)