Starting phenix.real_space_refine
on Thu Sep 18 01:02:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cq1_45806/09_2025/9cq1_45806.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cq1_45806/09_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_45806/09_2025/9cq1_45806.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cq1_45806/09_2025/9cq1_45806.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cq1_45806/09_2025/9cq1_45806.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cq1_45806/09_2025/9cq1_45806.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.46, per 1000 atoms: 0.27
  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: 1.02
  Conformation dependent library (CDL) restraints added in 880.6 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  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: 0.87
  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: 3.13

  Time building geometry restraints manager: 1.31 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: 0.03
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:             15.540
  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:          0.470
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.630
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.160
-------------------------------------------------------------------------------
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 : 4.52
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.008   0.002   ARG B 490 
 TYR   0.112   0.011   TYR B 298 
 PHE   0.042   0.007   PHE A 169 
 TRP   0.039   0.009   TRP B 733 
 HIS   0.006   0.002   HIS B 473 

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

*********************** 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  : 0.486 
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: 0.1386
  time to fit residues: 85.6620
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  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    7.9990
   chunk 149 optimal weight:    0.9980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 371 HIS
A 464 GLN
A 705 HIS
B 464 GLN
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 = 0.4196 r_free = 0.4196 target = 0.126420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.097718 restraints weight = 44046.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.100644 restraints weight = 33987.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.102942 restraints weight = 27363.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.104703 restraints weight = 22878.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.106067 restraints weight = 19706.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6794
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  13242  Z= 0.148
  Angle     :  0.623   8.971  17966  Z= 0.327
  Chirality :  0.047   0.281   1988
  Planarity :  0.005   0.060   2340
  Dihedral  :  4.670  15.863   1812
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.70 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.20), residues: 1690
  helix:  0.92 (0.19), residues: 714
  sheet:  0.24 (0.34), residues: 228
  loop :  0.62 (0.23), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 148 
 TYR   0.019   0.002   TYR A 298 
 PHE   0.022   0.002   PHE B 311 
 TRP   0.018   0.002   TRP B 627 
 HIS   0.008   0.001   HIS A 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (13242)
  covalent geometry    : angle       0.62257 (17966)
  hydrogen bonds       : bond        0.04650 (  602)
  hydrogen bonds       : angle       5.44289 ( 1728)

*********************** 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
  311 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 308
  time to evaluate  : 0.519 
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: A   57 MET cc_start: 0.8065 (mpp) cc_final: 0.7354 (mpp)
REVERT: A   79 LEU cc_start: 0.8824 (mt) cc_final: 0.8616 (mm)
REVERT: A  107 LEU cc_start: 0.9551 (tp) cc_final: 0.9067 (tp)
REVERT: A  108 LEU cc_start: 0.9349 (mt) cc_final: 0.9146 (mt)
REVERT: A  109 GLU cc_start: 0.8602 (tt0) cc_final: 0.7514 (tt0)
REVERT: A  111 CYS cc_start: 0.9160 (m) cc_final: 0.8935 (m)
REVERT: A  197 MET cc_start: 0.8786 (mtp) cc_final: 0.8150 (mmt)
REVERT: A  220 LYS cc_start: 0.9647 (tptt) cc_final: 0.9417 (tppt)
REVERT: A  270 VAL cc_start: 0.9111 (t) cc_final: 0.8817 (p)
REVERT: A  370 MET cc_start: 0.8427 (mtt) cc_final: 0.8108 (mtp)
REVERT: A  487 MET cc_start: 0.8473 (mmp) cc_final: 0.8254 (mmt)
REVERT: A  518 TYR cc_start: 0.8357 (m-80) cc_final: 0.7931 (m-80)
REVERT: A  528 MET cc_start: 0.7401 (pmm) cc_final: 0.7155 (pmm)
REVERT: A  575 PHE cc_start: 0.8650 (m-10) cc_final: 0.8393 (m-80)
REVERT: A  649 TRP cc_start: 0.7335 (t-100) cc_final: 0.6598 (t60)
REVERT: A  767 HIS cc_start: 0.8700 (t70) cc_final: 0.8407 (t70)
REVERT: A  820 SER cc_start: 0.9365 (m) cc_final: 0.9029 (p)
REVERT: B   57 MET cc_start: 0.8209 (mpp) cc_final: 0.7534 (mpp)
REVERT: B   92 LEU cc_start: 0.8424 (mt) cc_final: 0.8204 (mt)
REVERT: B   96 GLN cc_start: 0.8978 (mm110) cc_final: 0.8645 (mm110)
REVERT: B  107 LEU cc_start: 0.9663 (tp) cc_final: 0.9348 (tp)
REVERT: B  197 MET cc_start: 0.8710 (mmm) cc_final: 0.8205 (mmm)
REVERT: B  270 VAL cc_start: 0.9326 (t) cc_final: 0.9014 (p)
REVERT: B  294 MET cc_start: 0.8867 (mtm) cc_final: 0.8312 (mtm)
REVERT: B  306 LYS cc_start: 0.9213 (pttt) cc_final: 0.9010 (ptmt)
REVERT: B  333 MET cc_start: 0.6839 (mmm) cc_final: 0.6370 (mtp)
REVERT: B  532 LEU cc_start: 0.9349 (mm) cc_final: 0.9092 (mt)
REVERT: B  702 ILE cc_start: 0.9343 (mp) cc_final: 0.8995 (mp)
REVERT: B  760 LEU cc_start: 0.7740 (tp) cc_final: 0.7434 (mm)
REVERT: B  770 LEU cc_start: 0.8819 (mt) cc_final: 0.8580 (mt)
REVERT: B  796 LEU cc_start: 0.8469 (mt) cc_final: 0.8034 (mt)
  outliers start: 3
  outliers final: 0
  residues processed: 308
  average time/residue: 0.1166
  time to fit residues: 52.4994
Evaluate side-chains
  213 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 126 optimal weight:    7.9990
   chunk 35 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 163 optimal weight:    0.9980
   chunk 132 optimal weight:    0.2980
   chunk 148 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 50 optimal weight:    0.3980
   chunk 89 optimal weight:   10.0000
   chunk 83 optimal weight:    8.9990
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 371 HIS
** B 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 771 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.125535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.098009 restraints weight = 45303.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.100977 restraints weight = 34393.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.103207 restraints weight = 27341.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.104926 restraints weight = 22721.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.106364 restraints weight = 19532.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6838
moved from start:          0.3815

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= 0.120
  Angle     :  0.571   9.016  17966  Z= 0.296
  Chirality :  0.044   0.175   1988
  Planarity :  0.004   0.038   2340
  Dihedral  :  4.361  14.871   1812
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.85 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.20), residues: 1690
  helix:  1.07 (0.20), residues: 710
  sheet: -0.02 (0.33), residues: 234
  loop :  0.76 (0.23), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 794 
 TYR   0.019   0.002   TYR A 298 
 PHE   0.019   0.002   PHE A 311 
 TRP   0.030   0.002   TRP A 865 
 HIS   0.006   0.001   HIS A 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (13242)
  covalent geometry    : angle       0.57127 (17966)
  hydrogen bonds       : bond        0.04122 (  602)
  hydrogen bonds       : angle       5.15647 ( 1728)

*********************** 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
  287 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 284
  time to evaluate  : 0.543 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 MET cc_start: 0.8128 (mpp) cc_final: 0.7494 (mpp)
REVERT: A   79 LEU cc_start: 0.8791 (mt) cc_final: 0.8587 (mm)
REVERT: A  107 LEU cc_start: 0.9460 (tp) cc_final: 0.9127 (tp)
REVERT: A  108 LEU cc_start: 0.9409 (mt) cc_final: 0.9170 (mt)
REVERT: A  111 CYS cc_start: 0.9249 (m) cc_final: 0.9001 (m)
REVERT: A  150 ASP cc_start: 0.8719 (m-30) cc_final: 0.7921 (t70)
REVERT: A  197 MET cc_start: 0.8773 (mtp) cc_final: 0.8379 (mmm)
REVERT: A  220 LYS cc_start: 0.9642 (tptt) cc_final: 0.9401 (tppt)
REVERT: A  263 ILE cc_start: 0.8123 (mt) cc_final: 0.7881 (mt)
REVERT: A  270 VAL cc_start: 0.9202 (t) cc_final: 0.8831 (p)
REVERT: A  333 MET cc_start: 0.7546 (mmm) cc_final: 0.7132 (mtp)
REVERT: A  370 MET cc_start: 0.8562 (mtt) cc_final: 0.8300 (mtp)
REVERT: A  462 GLU cc_start: 0.9162 (tt0) cc_final: 0.8527 (tt0)
REVERT: A  767 HIS cc_start: 0.8859 (t70) cc_final: 0.8645 (t70)
REVERT: A  768 GLU cc_start: 0.8909 (mp0) cc_final: 0.8619 (mp0)
REVERT: A  820 SER cc_start: 0.9328 (m) cc_final: 0.9029 (p)
REVERT: A  831 LEU cc_start: 0.7772 (pp) cc_final: 0.7559 (pp)
REVERT: B  107 LEU cc_start: 0.9660 (tp) cc_final: 0.9344 (tp)
REVERT: B  108 LEU cc_start: 0.9451 (mt) cc_final: 0.9212 (mt)
REVERT: B  197 MET cc_start: 0.8687 (mmm) cc_final: 0.8319 (mmm)
REVERT: B  227 MET cc_start: 0.8263 (mmp) cc_final: 0.7990 (mmp)
REVERT: B  294 MET cc_start: 0.9299 (mtm) cc_final: 0.8430 (mmm)
REVERT: B  333 MET cc_start: 0.7031 (mmm) cc_final: 0.6823 (mtp)
REVERT: B  447 THR cc_start: 0.7937 (p) cc_final: 0.7733 (p)
REVERT: B  577 CYS cc_start: 0.8836 (m) cc_final: 0.8559 (t)
REVERT: B  579 THR cc_start: 0.9042 (p) cc_final: 0.8783 (p)
REVERT: B  582 GLN cc_start: 0.9370 (mt0) cc_final: 0.8965 (mt0)
REVERT: B  767 HIS cc_start: 0.8414 (t70) cc_final: 0.7965 (t70)
REVERT: B  770 LEU cc_start: 0.8800 (mt) cc_final: 0.8299 (mt)
REVERT: B  796 LEU cc_start: 0.8450 (mt) cc_final: 0.8080 (mt)
  outliers start: 3
  outliers final: 0
  residues processed: 284
  average time/residue: 0.1041
  time to fit residues: 44.8492
Evaluate side-chains
  224 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   chunk 68 optimal weight:    9.9990
   chunk 167 optimal weight:    8.9990
   chunk 147 optimal weight:    5.9990
   chunk 119 optimal weight:    9.9990
   chunk 10 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0570
   chunk 20 optimal weight:    8.9990
   chunk 45 optimal weight:    9.9990
   chunk 107 optimal weight:    9.9990
   overall best weight:    5.2106

-------------------------------------------------------------------------------
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 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 582 GLN
A 705 HIS
** A 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 785 HIS
A 806 GLN
B 350 ASN
** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 806 GLN ** 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 = 0.3837 r_free = 0.3837 target = 0.103539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.080224 restraints weight = 50649.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.082526 restraints weight = 37858.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.084286 restraints weight = 30193.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.085649 restraints weight = 25019.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.086670 restraints weight = 21572.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.6624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.085  13242  Z= 0.336
  Angle     :  0.899  11.107  17966  Z= 0.471
  Chirality :  0.051   0.215   1988
  Planarity :  0.008   0.218   2340
  Dihedral  :  5.798  27.179   1812
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 25.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.20), residues: 1690
  helix: -0.09 (0.18), residues: 716
  sheet:  0.16 (0.40), residues: 198
  loop :  0.34 (0.23), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 794 
 TYR   0.025   0.003   TYR A 330 
 PHE   0.025   0.003   PHE A 311 
 TRP   0.038   0.004   TRP A 859 
 HIS   0.012   0.003   HIS B 423 

Details of bonding type rmsd
  covalent geometry    : bond        0.00701 (13242)
  covalent geometry    : angle       0.89925 (17966)
  hydrogen bonds       : bond        0.05659 (  602)
  hydrogen bonds       : angle       6.71454 ( 1728)

*********************** 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
  258 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 0.508 
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: A   96 GLN cc_start: 0.9097 (mp10) cc_final: 0.8860 (mp10)
REVERT: A  107 LEU cc_start: 0.9636 (tp) cc_final: 0.9273 (tp)
REVERT: A  108 LEU cc_start: 0.9645 (mt) cc_final: 0.9404 (mt)
REVERT: A  109 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8053 (tm-30)
REVERT: A  111 CYS cc_start: 0.9410 (m) cc_final: 0.9203 (m)
REVERT: A  197 MET cc_start: 0.9155 (mtp) cc_final: 0.8821 (mmm)
REVERT: A  220 LYS cc_start: 0.9574 (tptt) cc_final: 0.9334 (tppt)
REVERT: A  410 MET cc_start: 0.8769 (mmt) cc_final: 0.8204 (mmm)
REVERT: A  483 PRO cc_start: 0.8610 (Cg_exo) cc_final: 0.8377 (Cg_endo)
REVERT: A  495 LEU cc_start: 0.9356 (mt) cc_final: 0.9107 (mm)
REVERT: A  575 PHE cc_start: 0.8920 (m-80) cc_final: 0.8598 (m-80)
REVERT: A  733 TRP cc_start: 0.8103 (t60) cc_final: 0.7629 (t-100)
REVERT: A  767 HIS cc_start: 0.8749 (t70) cc_final: 0.8443 (t70)
REVERT: A  844 VAL cc_start: 0.8862 (m) cc_final: 0.8641 (p)
REVERT: B   57 MET cc_start: 0.8697 (mpp) cc_final: 0.8224 (mpp)
REVERT: B   92 LEU cc_start: 0.9037 (mt) cc_final: 0.8574 (mt)
REVERT: B   96 GLN cc_start: 0.8928 (mm110) cc_final: 0.8268 (mt0)
REVERT: B  107 LEU cc_start: 0.9688 (tp) cc_final: 0.9365 (tp)
REVERT: B  108 LEU cc_start: 0.9673 (mt) cc_final: 0.9401 (mt)
REVERT: B  112 TYR cc_start: 0.9414 (t80) cc_final: 0.9183 (t80)
REVERT: B  113 GLU cc_start: 0.8617 (mp0) cc_final: 0.8182 (mm-30)
REVERT: B  150 ASP cc_start: 0.8364 (m-30) cc_final: 0.8007 (m-30)
REVERT: B  197 MET cc_start: 0.9007 (mmm) cc_final: 0.8487 (mmm)
REVERT: B  449 SER cc_start: 0.8060 (m) cc_final: 0.7744 (p)
REVERT: B  487 MET cc_start: 0.9096 (mmp) cc_final: 0.8895 (mmt)
REVERT: B  577 CYS cc_start: 0.9069 (m) cc_final: 0.8666 (t)
REVERT: B  579 THR cc_start: 0.9304 (p) cc_final: 0.9025 (p)
REVERT: B  581 ILE cc_start: 0.9328 (mt) cc_final: 0.9115 (mt)
REVERT: B  582 GLN cc_start: 0.9342 (mt0) cc_final: 0.9005 (mt0)
REVERT: B  727 LYS cc_start: 0.7360 (mttt) cc_final: 0.7105 (mmtt)
REVERT: B  733 TRP cc_start: 0.8483 (t60) cc_final: 0.8196 (t-100)
REVERT: B  844 VAL cc_start: 0.8731 (m) cc_final: 0.8517 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 258
  average time/residue: 0.1059
  time to fit residues: 40.8579
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  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 72 optimal weight:    9.9990
   chunk 85 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 7 optimal weight:    9.9990
   chunk 165 optimal weight:    9.9990
   chunk 4 optimal weight:    7.9990
   chunk 110 optimal weight:    5.9990
   chunk 113 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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**
B 195 GLN
B 350 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 771 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 = 0.3832 r_free = 0.3832 target = 0.102684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.079631 restraints weight = 49762.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.082022 restraints weight = 36968.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.083762 restraints weight = 29156.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.085161 restraints weight = 24175.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.086177 restraints weight = 20741.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.7331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  13242  Z= 0.242
  Angle     :  0.723  11.192  17966  Z= 0.374
  Chirality :  0.046   0.193   1988
  Planarity :  0.006   0.134   2340
  Dihedral  :  5.203  21.790   1812
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 20.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.34 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.20), residues: 1690
  helix: -0.01 (0.18), residues: 718
  sheet:  0.13 (0.38), residues: 206
  loop :  0.25 (0.23), residues: 766

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG B 262 
 TYR   0.017   0.002   TYR A 298 
 PHE   0.031   0.002   PHE A 818 
 TRP   0.025   0.003   TRP A 145 
 HIS   0.007   0.002   HIS B 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 (13242)
  covalent geometry    : angle       0.72265 (17966)
  hydrogen bonds       : bond        0.04735 (  602)
  hydrogen bonds       : angle       6.24151 ( 1728)

*********************** 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
  238 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 237
  time to evaluate  : 0.518 
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: 0.9072 (mp10) cc_final: 0.8784 (mp10)
REVERT: A   99 MET cc_start: 0.8658 (mmp) cc_final: 0.8298 (tpp)
REVERT: A  108 LEU cc_start: 0.9666 (mt) cc_final: 0.9439 (mt)
REVERT: A  109 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8159 (tm-30)
REVERT: A  145 TRP cc_start: 0.7836 (m-10) cc_final: 0.7591 (m-10)
REVERT: A  197 MET cc_start: 0.9147 (mtp) cc_final: 0.8907 (mmm)
REVERT: A  220 LYS cc_start: 0.9565 (tptt) cc_final: 0.9333 (tppt)
REVERT: A  290 GLN cc_start: 0.8678 (mt0) cc_final: 0.8290 (mp10)
REVERT: A  294 MET cc_start: 0.9602 (mtt) cc_final: 0.9338 (mmm)
REVERT: A  303 LEU cc_start: 0.8436 (tp) cc_final: 0.8071 (tt)
REVERT: A  410 MET cc_start: 0.8568 (mmt) cc_final: 0.8187 (mmm)
REVERT: A  417 MET cc_start: 0.8591 (ptp) cc_final: 0.8366 (pmm)
REVERT: A  528 MET cc_start: 0.8092 (pmm) cc_final: 0.7851 (pmm)
REVERT: A  575 PHE cc_start: 0.8952 (m-80) cc_final: 0.8622 (m-80)
REVERT: A  582 GLN cc_start: 0.9465 (tp-100) cc_final: 0.9257 (tp-100)
REVERT: A  756 HIS cc_start: 0.9254 (m-70) cc_final: 0.9042 (m90)
REVERT: A  767 HIS cc_start: 0.8754 (t70) cc_final: 0.8273 (t70)
REVERT: A  770 LEU cc_start: 0.9064 (mt) cc_final: 0.8745 (mt)
REVERT: A  854 MET cc_start: 0.9202 (ptp) cc_final: 0.8985 (ptp)
REVERT: B   57 MET cc_start: 0.8769 (mpp) cc_final: 0.8294 (mpp)
REVERT: B   92 LEU cc_start: 0.9075 (mt) cc_final: 0.8871 (mt)
REVERT: B   96 GLN cc_start: 0.9015 (mm110) cc_final: 0.8570 (mm-40)
REVERT: B   99 MET cc_start: 0.8333 (tpp) cc_final: 0.8066 (tpp)
REVERT: B  108 LEU cc_start: 0.9663 (mt) cc_final: 0.9461 (mt)
REVERT: B  113 GLU cc_start: 0.8498 (mp0) cc_final: 0.8233 (mm-30)
REVERT: B  197 MET cc_start: 0.9075 (mmm) cc_final: 0.8800 (tpp)
REVERT: B  290 GLN cc_start: 0.8654 (mt0) cc_final: 0.8258 (mp10)
REVERT: B  294 MET cc_start: 0.9589 (mtt) cc_final: 0.9182 (mmm)
REVERT: B  333 MET cc_start: 0.7744 (mtp) cc_final: 0.7213 (mtp)
REVERT: B  360 MET cc_start: 0.9302 (mmm) cc_final: 0.8707 (tpp)
REVERT: B  487 MET cc_start: 0.9241 (mmp) cc_final: 0.8995 (mmp)
REVERT: B  579 THR cc_start: 0.9369 (p) cc_final: 0.9083 (p)
REVERT: B  582 GLN cc_start: 0.9395 (mt0) cc_final: 0.9116 (mt0)
REVERT: B  687 LEU cc_start: 0.8262 (mt) cc_final: 0.8058 (mt)
REVERT: B  727 LYS cc_start: 0.7522 (mttt) cc_final: 0.7310 (mmtt)
REVERT: B  733 TRP cc_start: 0.8199 (t60) cc_final: 0.7904 (t60)
REVERT: B  756 HIS cc_start: 0.9411 (m-70) cc_final: 0.9193 (m90)
  outliers start: 1
  outliers final: 0
  residues processed: 238
  average time/residue: 0.1103
  time to fit residues: 39.1895
Evaluate side-chains
  170 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 125 optimal weight:    2.9990
   chunk 106 optimal weight:    8.9990
   chunk 5 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 66 optimal weight:    2.9990
   chunk 164 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 167 optimal weight:    3.9990
   chunk 146 optimal weight:    6.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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**
** B 378 ASN ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.101807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.078781 restraints weight = 49346.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.081059 restraints weight = 36885.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.082791 restraints weight = 29417.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.084100 restraints weight = 24404.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.085198 restraints weight = 21063.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.8051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  13242  Z= 0.205
  Angle     :  0.695   9.199  17966  Z= 0.360
  Chirality :  0.046   0.172   1988
  Planarity :  0.005   0.083   2340
  Dihedral  :  5.152  23.823   1812
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 20.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.02 (0.21), residues: 1690
  helix:  0.07 (0.19), residues: 720
  sheet: -0.27 (0.38), residues: 212
  loop :  0.28 (0.24), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 451 
 TYR   0.015   0.002   TYR A 298 
 PHE   0.028   0.002   PHE A 311 
 TRP   0.023   0.002   TRP A 859 
 HIS   0.009   0.001   HIS B 785 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (13242)
  covalent geometry    : angle       0.69486 (17966)
  hydrogen bonds       : bond        0.04566 (  602)
  hydrogen bonds       : angle       6.07175 ( 1728)

*********************** 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
  233 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.527 
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   57 MET cc_start: 0.8747 (mpp) cc_final: 0.7883 (mpp)
REVERT: A   96 GLN cc_start: 0.9075 (mp10) cc_final: 0.8844 (mp10)
REVERT: A   99 MET cc_start: 0.8638 (mmp) cc_final: 0.8235 (tpp)
REVERT: A  108 LEU cc_start: 0.9680 (mt) cc_final: 0.9464 (mt)
REVERT: A  109 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8097 (tm-30)
REVERT: A  197 MET cc_start: 0.9172 (mtp) cc_final: 0.8902 (mmm)
REVERT: A  220 LYS cc_start: 0.9573 (tptt) cc_final: 0.9334 (tppt)
REVERT: A  290 GLN cc_start: 0.8760 (mt0) cc_final: 0.8371 (mp10)
REVERT: A  294 MET cc_start: 0.9622 (mtt) cc_final: 0.9395 (mmm)
REVERT: A  303 LEU cc_start: 0.8616 (tp) cc_final: 0.8237 (tt)
REVERT: A  575 PHE cc_start: 0.9020 (m-80) cc_final: 0.8707 (m-80)
REVERT: A  673 ILE cc_start: 0.8540 (pt) cc_final: 0.8213 (pt)
REVERT: A  732 ARG cc_start: 0.8945 (mpt180) cc_final: 0.8629 (mmt-90)
REVERT: A  756 HIS cc_start: 0.9271 (m-70) cc_final: 0.9043 (m90)
REVERT: A  767 HIS cc_start: 0.8805 (t70) cc_final: 0.8420 (t70)
REVERT: A  770 LEU cc_start: 0.9022 (mt) cc_final: 0.8768 (mt)
REVERT: B   40 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8565 (mp0)
REVERT: B   57 MET cc_start: 0.8848 (mpp) cc_final: 0.7692 (mpp)
REVERT: B   96 GLN cc_start: 0.9092 (mm110) cc_final: 0.8622 (mm110)
REVERT: B   99 MET cc_start: 0.8377 (tpp) cc_final: 0.8165 (tpp)
REVERT: B  113 GLU cc_start: 0.8670 (mp0) cc_final: 0.8071 (mm-30)
REVERT: B  197 MET cc_start: 0.9090 (mmm) cc_final: 0.8812 (tpp)
REVERT: B  225 MET cc_start: 0.8374 (mmt) cc_final: 0.7959 (mmt)
REVERT: B  290 GLN cc_start: 0.8690 (mt0) cc_final: 0.8332 (mp10)
REVERT: B  303 LEU cc_start: 0.8400 (tp) cc_final: 0.8022 (tt)
REVERT: B  333 MET cc_start: 0.7986 (mtp) cc_final: 0.7585 (mtp)
REVERT: B  360 MET cc_start: 0.9329 (mmm) cc_final: 0.8804 (tpp)
REVERT: B  410 MET cc_start: 0.8856 (mtt) cc_final: 0.8495 (mmm)
REVERT: B  417 MET cc_start: 0.8511 (ptp) cc_final: 0.8277 (pmm)
REVERT: B  487 MET cc_start: 0.9117 (mmp) cc_final: 0.8860 (mmt)
REVERT: B  533 MET cc_start: 0.8569 (tpt) cc_final: 0.8247 (tpp)
REVERT: B  579 THR cc_start: 0.9440 (p) cc_final: 0.9177 (p)
REVERT: B  582 GLN cc_start: 0.9407 (mt0) cc_final: 0.9058 (mt0)
REVERT: B  592 MET cc_start: 0.9571 (mmm) cc_final: 0.9265 (mmm)
REVERT: B  642 MET cc_start: 0.7261 (mpp) cc_final: 0.6996 (mpp)
REVERT: B  727 LYS cc_start: 0.7727 (mttt) cc_final: 0.7489 (mmtt)
REVERT: B  733 TRP cc_start: 0.8212 (t60) cc_final: 0.7934 (t60)
REVERT: B  770 LEU cc_start: 0.8976 (mt) cc_final: 0.8742 (mt)
REVERT: B  785 HIS cc_start: 0.7629 (t-90) cc_final: 0.7214 (t-90)
REVERT: B  855 VAL cc_start: 0.9137 (p) cc_final: 0.8298 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 233
  average time/residue: 0.1102
  time to fit residues: 38.5595
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  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 126 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9980
   chunk 68 optimal weight:    3.9990
   chunk 127 optimal weight:    3.9990
   chunk 148 optimal weight:    2.9990
   chunk 109 optimal weight:    0.4980
   chunk 61 optimal weight:    0.8980
   chunk 141 optimal weight:    5.9990
   chunk 159 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 146 optimal weight:    3.9990
   overall best weight:    1.8784

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.103867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.080475 restraints weight = 49077.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.082870 restraints weight = 36452.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.084680 restraints weight = 28720.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.086066 restraints weight = 23810.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.087080 restraints weight = 20476.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.8295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13242  Z= 0.157
  Angle     :  0.660  11.719  17966  Z= 0.335
  Chirality :  0.045   0.182   1988
  Planarity :  0.005   0.054   2340
  Dihedral  :  4.914  21.706   1812
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 18.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.21), residues: 1690
  helix:  0.32 (0.19), residues: 718
  sheet: -0.62 (0.34), residues: 238
  loop :  0.38 (0.24), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  48 
 TYR   0.014   0.002   TYR B 112 
 PHE   0.019   0.002   PHE A 311 
 TRP   0.024   0.002   TRP A 145 
 HIS   0.008   0.001   HIS B 785 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (13242)
  covalent geometry    : angle       0.65964 (17966)
  hydrogen bonds       : bond        0.04143 (  602)
  hydrogen bonds       : angle       5.81644 ( 1728)

*********************** 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
  243 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8419 (mp0)
REVERT: A   57 MET cc_start: 0.8742 (mpp) cc_final: 0.7087 (mpp)
REVERT: A   96 GLN cc_start: 0.8961 (mp10) cc_final: 0.8712 (mp10)
REVERT: A   99 MET cc_start: 0.8511 (mmp) cc_final: 0.8170 (tpp)
REVERT: A  108 LEU cc_start: 0.9667 (mt) cc_final: 0.9465 (mt)
REVERT: A  197 MET cc_start: 0.9123 (mtp) cc_final: 0.8902 (tpp)
REVERT: A  220 LYS cc_start: 0.9588 (tptt) cc_final: 0.9355 (tppt)
REVERT: A  290 GLN cc_start: 0.8720 (mt0) cc_final: 0.8366 (mp10)
REVERT: A  303 LEU cc_start: 0.8561 (tp) cc_final: 0.8192 (tt)
REVERT: A  313 CYS cc_start: 0.7942 (m) cc_final: 0.7559 (t)
REVERT: A  333 MET cc_start: 0.7996 (mtp) cc_final: 0.7760 (mtp)
REVERT: A  410 MET cc_start: 0.8458 (mmt) cc_final: 0.8177 (mmm)
REVERT: A  470 MET cc_start: 0.8306 (pmm) cc_final: 0.7847 (pmm)
REVERT: A  495 LEU cc_start: 0.9375 (mt) cc_final: 0.9091 (mm)
REVERT: A  575 PHE cc_start: 0.9037 (m-80) cc_final: 0.8745 (m-80)
REVERT: A  733 TRP cc_start: 0.8155 (t60) cc_final: 0.7733 (t-100)
REVERT: A  767 HIS cc_start: 0.8857 (t70) cc_final: 0.8477 (t70)
REVERT: A  770 LEU cc_start: 0.8992 (mt) cc_final: 0.8750 (mt)
REVERT: B   40 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8540 (mp0)
REVERT: B   57 MET cc_start: 0.8876 (mpp) cc_final: 0.7713 (mpp)
REVERT: B   96 GLN cc_start: 0.9111 (mm110) cc_final: 0.8717 (mm110)
REVERT: B  113 GLU cc_start: 0.8638 (mp0) cc_final: 0.8174 (mm-30)
REVERT: B  197 MET cc_start: 0.9066 (mmm) cc_final: 0.8795 (tpp)
REVERT: B  290 GLN cc_start: 0.8686 (mt0) cc_final: 0.8355 (mp10)
REVERT: B  303 LEU cc_start: 0.8388 (tp) cc_final: 0.8005 (tt)
REVERT: B  333 MET cc_start: 0.7955 (mtp) cc_final: 0.7739 (mtp)
REVERT: B  360 MET cc_start: 0.9297 (mmm) cc_final: 0.8755 (tpp)
REVERT: B  410 MET cc_start: 0.8802 (mtt) cc_final: 0.8386 (mmm)
REVERT: B  448 TYR cc_start: 0.9314 (t80) cc_final: 0.8793 (t80)
REVERT: B  487 MET cc_start: 0.9110 (mmp) cc_final: 0.8818 (mmt)
REVERT: B  579 THR cc_start: 0.9454 (p) cc_final: 0.9185 (p)
REVERT: B  582 GLN cc_start: 0.9413 (mt0) cc_final: 0.9061 (mt0)
REVERT: B  592 MET cc_start: 0.9569 (mmm) cc_final: 0.9210 (mmm)
REVERT: B  649 TRP cc_start: 0.7916 (t-100) cc_final: 0.7527 (t-100)
REVERT: B  727 LYS cc_start: 0.7730 (mttt) cc_final: 0.7504 (mmtt)
REVERT: B  733 TRP cc_start: 0.8149 (t60) cc_final: 0.7939 (t60)
REVERT: B  770 LEU cc_start: 0.8916 (mt) cc_final: 0.8671 (mt)
REVERT: B  785 HIS cc_start: 0.7503 (t-90) cc_final: 0.7170 (t-90)
REVERT: B  855 VAL cc_start: 0.9031 (p) cc_final: 0.8626 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.1014
  time to fit residues: 37.6813
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  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 128 optimal weight:    4.9990
   chunk 10 optimal weight:   10.0000
   chunk 144 optimal weight:   20.0000
   chunk 152 optimal weight:    7.9990
   chunk 62 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 73 optimal weight:    0.5980
   chunk 61 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 136 optimal weight:    4.9990
   chunk 129 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 655 GLN
** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 756 HIS
** B 785 HIS ** 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 = 0.3875 r_free = 0.3875 target = 0.105226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.082044 restraints weight = 46112.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.084464 restraints weight = 34121.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.086344 restraints weight = 26749.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.087806 restraints weight = 22009.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.088935 restraints weight = 18764.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.8429

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= 0.129
  Angle     :  0.650  10.250  17966  Z= 0.329
  Chirality :  0.045   0.204   1988
  Planarity :  0.004   0.050   2340
  Dihedral  :  4.656  20.165   1812
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.21), residues: 1690
  helix:  0.47 (0.19), residues: 716
  sheet: -0.64 (0.33), residues: 252
  loop :  0.46 (0.25), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 794 
 TYR   0.014   0.001   TYR A  38 
 PHE   0.020   0.002   PHE B 818 
 TRP   0.029   0.002   TRP B 627 
 HIS   0.007   0.001   HIS B 466 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (13242)
  covalent geometry    : angle       0.65015 (17966)
  hydrogen bonds       : bond        0.03972 (  602)
  hydrogen bonds       : angle       5.63185 ( 1728)

*********************** 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
  250 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8384 (mp0)
REVERT: A   57 MET cc_start: 0.8669 (mpp) cc_final: 0.7522 (mpp)
REVERT: A   96 GLN cc_start: 0.8954 (mp10) cc_final: 0.8650 (pm20)
REVERT: A  109 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7654 (tm-30)
REVERT: A  197 MET cc_start: 0.9054 (mtp) cc_final: 0.8840 (mmm)
REVERT: A  220 LYS cc_start: 0.9579 (tptt) cc_final: 0.9339 (tppt)
REVERT: A  225 MET cc_start: 0.8011 (mmt) cc_final: 0.7551 (mmt)
REVERT: A  290 GLN cc_start: 0.8732 (mt0) cc_final: 0.8366 (mp10)
REVERT: A  303 LEU cc_start: 0.8456 (tp) cc_final: 0.8098 (tt)
REVERT: A  313 CYS cc_start: 0.7959 (m) cc_final: 0.7531 (t)
REVERT: A  406 SER cc_start: 0.8210 (p) cc_final: 0.7759 (t)
REVERT: A  470 MET cc_start: 0.8248 (pmm) cc_final: 0.7833 (pmm)
REVERT: A  575 PHE cc_start: 0.9016 (m-80) cc_final: 0.8677 (m-80)
REVERT: A  577 CYS cc_start: 0.9219 (t) cc_final: 0.8965 (p)
REVERT: A  756 HIS cc_start: 0.9138 (m-70) cc_final: 0.8517 (m90)
REVERT: A  767 HIS cc_start: 0.8868 (t70) cc_final: 0.8488 (t70)
REVERT: A  770 LEU cc_start: 0.8923 (mt) cc_final: 0.8657 (mt)
REVERT: A  854 MET cc_start: 0.8981 (ptp) cc_final: 0.8641 (ptp)
REVERT: B   40 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8526 (mp0)
REVERT: B   57 MET cc_start: 0.8856 (mpp) cc_final: 0.7588 (mpp)
REVERT: B  113 GLU cc_start: 0.8675 (mp0) cc_final: 0.7904 (mm-30)
REVERT: B  197 MET cc_start: 0.9056 (mmm) cc_final: 0.8794 (tpp)
REVERT: B  225 MET cc_start: 0.8207 (mmt) cc_final: 0.7866 (mmt)
REVERT: B  290 GLN cc_start: 0.8673 (mt0) cc_final: 0.8353 (mp10)
REVERT: B  294 MET cc_start: 0.9397 (mmm) cc_final: 0.9123 (mmm)
REVERT: B  303 LEU cc_start: 0.8293 (tp) cc_final: 0.7919 (tt)
REVERT: B  360 MET cc_start: 0.9313 (mmm) cc_final: 0.8746 (tpp)
REVERT: B  410 MET cc_start: 0.8727 (mtt) cc_final: 0.8383 (mmm)
REVERT: B  448 TYR cc_start: 0.9291 (t80) cc_final: 0.8785 (t80)
REVERT: B  476 CYS cc_start: 0.9186 (m) cc_final: 0.8984 (m)
REVERT: B  487 MET cc_start: 0.9069 (mmp) cc_final: 0.8793 (mmt)
REVERT: B  579 THR cc_start: 0.9442 (p) cc_final: 0.9141 (p)
REVERT: B  582 GLN cc_start: 0.9396 (mt0) cc_final: 0.9012 (mt0)
REVERT: B  592 MET cc_start: 0.9546 (mmm) cc_final: 0.9256 (mmm)
REVERT: B  649 TRP cc_start: 0.7975 (t-100) cc_final: 0.7620 (t-100)
REVERT: B  727 LYS cc_start: 0.7766 (mttt) cc_final: 0.7526 (mmtt)
REVERT: B  770 LEU cc_start: 0.8889 (mt) cc_final: 0.8645 (mt)
REVERT: B  785 HIS cc_start: 0.7416 (t-90) cc_final: 0.7097 (t-90)
REVERT: B  855 VAL cc_start: 0.8919 (p) cc_final: 0.8350 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 250
  average time/residue: 0.1027
  time to fit residues: 39.8198
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  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 75 optimal weight:    9.9990
   chunk 157 optimal weight:   10.0000
   chunk 106 optimal weight:   10.0000
   chunk 127 optimal weight:    8.9990
   chunk 158 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 150 optimal weight:    4.9990
   chunk 152 optimal weight:    1.9990
   chunk 130 optimal weight:   20.0000
   chunk 6 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.099089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.076585 restraints weight = 50437.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.078881 restraints weight = 37291.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.080608 restraints weight = 29279.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.081919 restraints weight = 24234.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.082894 restraints weight = 20810.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.9118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  13242  Z= 0.247
  Angle     :  0.766  10.256  17966  Z= 0.397
  Chirality :  0.047   0.179   1988
  Planarity :  0.005   0.052   2340
  Dihedral  :  5.162  21.927   1812
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 23.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.21), residues: 1690
  helix:  0.05 (0.19), residues: 704
  sheet: -0.24 (0.38), residues: 200
  loop :  0.16 (0.23), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 628 
 TYR   0.026   0.002   TYR A 518 
 PHE   0.021   0.002   PHE A 311 
 TRP   0.076   0.003   TRP A 733 
 HIS   0.008   0.002   HIS B 785 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 (13242)
  covalent geometry    : angle       0.76571 (17966)
  hydrogen bonds       : bond        0.04687 (  602)
  hydrogen bonds       : angle       6.24549 ( 1728)

*********************** 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
  226 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.553 
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: 0.8778 (mpp) cc_final: 0.8229 (mpp)
REVERT: A  108 LEU cc_start: 0.9576 (mt) cc_final: 0.9347 (mt)
REVERT: A  197 MET cc_start: 0.9181 (mtp) cc_final: 0.8899 (tpp)
REVERT: A  220 LYS cc_start: 0.9573 (tptt) cc_final: 0.9323 (tppt)
REVERT: A  225 MET cc_start: 0.7842 (mmt) cc_final: 0.7439 (mmt)
REVERT: A  290 GLN cc_start: 0.8964 (mt0) cc_final: 0.8510 (mp10)
REVERT: A  303 LEU cc_start: 0.8659 (tp) cc_final: 0.8314 (tt)
REVERT: A  313 CYS cc_start: 0.7795 (m) cc_final: 0.7444 (t)
REVERT: A  360 MET cc_start: 0.9425 (tmm) cc_final: 0.9082 (ppp)
REVERT: A  470 MET cc_start: 0.8299 (pmm) cc_final: 0.7778 (pmm)
REVERT: A  538 PHE cc_start: 0.8170 (t80) cc_final: 0.7951 (t80)
REVERT: A  575 PHE cc_start: 0.9102 (m-80) cc_final: 0.8776 (m-80)
REVERT: A  577 CYS cc_start: 0.9260 (t) cc_final: 0.9029 (p)
REVERT: A  767 HIS cc_start: 0.8692 (t70) cc_final: 0.8125 (t70)
REVERT: A  770 LEU cc_start: 0.9086 (mt) cc_final: 0.8711 (mt)
REVERT: B   57 MET cc_start: 0.8873 (mpp) cc_final: 0.8265 (mpp)
REVERT: B   96 GLN cc_start: 0.9133 (mp10) cc_final: 0.8776 (mp10)
REVERT: B  197 MET cc_start: 0.9046 (mmm) cc_final: 0.8742 (tpp)
REVERT: B  225 MET cc_start: 0.8184 (mmt) cc_final: 0.7896 (mmt)
REVERT: B  303 LEU cc_start: 0.8497 (tp) cc_final: 0.8097 (tt)
REVERT: B  417 MET cc_start: 0.8953 (pmm) cc_final: 0.8380 (pmm)
REVERT: B  487 MET cc_start: 0.9138 (mmp) cc_final: 0.8851 (mmt)
REVERT: B  513 GLU cc_start: 0.8278 (tp30) cc_final: 0.7676 (tp30)
REVERT: B  579 THR cc_start: 0.9507 (p) cc_final: 0.9239 (p)
REVERT: B  582 GLN cc_start: 0.9409 (mt0) cc_final: 0.9029 (mt0)
REVERT: B  592 MET cc_start: 0.9633 (mmm) cc_final: 0.9231 (tpp)
REVERT: B  597 ASP cc_start: 0.9252 (m-30) cc_final: 0.9037 (t0)
REVERT: B  649 TRP cc_start: 0.7999 (t-100) cc_final: 0.7599 (t-100)
REVERT: B  727 LYS cc_start: 0.7996 (mttt) cc_final: 0.7745 (mmtt)
REVERT: B  770 LEU cc_start: 0.9027 (mt) cc_final: 0.8775 (mt)
REVERT: B  785 HIS cc_start: 0.7411 (t-90) cc_final: 0.7161 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 226
  average time/residue: 0.0970
  time to fit residues: 34.2967
Evaluate side-chains
  176 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 121 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 141 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 80 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 132 optimal weight:    0.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 466 HIS
** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 756 HIS
** B 785 HIS ** 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 = 0.3830 r_free = 0.3830 target = 0.101822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.079067 restraints weight = 47923.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.081433 restraints weight = 35505.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.083189 restraints weight = 27843.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.084602 restraints weight = 23009.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.085673 restraints weight = 19660.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.9239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13242  Z= 0.153
  Angle     :  0.689  12.909  17966  Z= 0.352
  Chirality :  0.046   0.190   1988
  Planarity :  0.005   0.076   2340
  Dihedral  :  4.899  18.391   1812
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 18.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.21), residues: 1690
  helix:  0.27 (0.19), residues: 704
  sheet: -0.76 (0.34), residues: 242
  loop :  0.37 (0.24), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 105 
 TYR   0.018   0.002   TYR A  38 
 PHE   0.020   0.002   PHE A 818 
 TRP   0.088   0.003   TRP B 733 
 HIS   0.007   0.001   HIS B 785 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (13242)
  covalent geometry    : angle       0.68887 (17966)
  hydrogen bonds       : bond        0.04221 (  602)
  hydrogen bonds       : angle       5.94334 ( 1728)

********************** 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
  236 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 MET cc_start: 0.8774 (mpp) cc_final: 0.8171 (mpp)
REVERT: A  108 LEU cc_start: 0.9500 (mt) cc_final: 0.9274 (mt)
REVERT: A  197 MET cc_start: 0.9117 (mtp) cc_final: 0.8670 (tpp)
REVERT: A  220 LYS cc_start: 0.9565 (tptt) cc_final: 0.9313 (tppt)
REVERT: A  290 GLN cc_start: 0.8874 (mt0) cc_final: 0.8522 (mp10)
REVERT: A  303 LEU cc_start: 0.8585 (tp) cc_final: 0.8248 (tt)
REVERT: A  313 CYS cc_start: 0.7767 (m) cc_final: 0.7475 (m)
REVERT: A  360 MET cc_start: 0.9424 (tmm) cc_final: 0.9092 (ppp)
REVERT: A  406 SER cc_start: 0.8286 (p) cc_final: 0.7874 (t)
REVERT: A  470 MET cc_start: 0.8308 (pmm) cc_final: 0.7878 (pmm)
REVERT: A  521 MET cc_start: 0.8844 (tmm) cc_final: 0.8347 (tpt)
REVERT: A  575 PHE cc_start: 0.9067 (m-80) cc_final: 0.8729 (m-80)
REVERT: A  577 CYS cc_start: 0.9310 (t) cc_final: 0.9058 (p)
REVERT: A  733 TRP cc_start: 0.8085 (t60) cc_final: 0.7733 (t-100)
REVERT: A  767 HIS cc_start: 0.8812 (t70) cc_final: 0.8387 (t70)
REVERT: A  770 LEU cc_start: 0.8978 (mt) cc_final: 0.8660 (mt)
REVERT: B   96 GLN cc_start: 0.9197 (mp10) cc_final: 0.8602 (mp10)
REVERT: B  197 MET cc_start: 0.9058 (mmm) cc_final: 0.8786 (tpp)
REVERT: B  225 MET cc_start: 0.8306 (mmt) cc_final: 0.7783 (mmt)
REVERT: B  290 GLN cc_start: 0.8778 (mt0) cc_final: 0.8456 (mp10)
REVERT: B  303 LEU cc_start: 0.8457 (tp) cc_final: 0.8045 (tt)
REVERT: B  417 MET cc_start: 0.8959 (pmm) cc_final: 0.8483 (pmm)
REVERT: B  448 TYR cc_start: 0.9273 (t80) cc_final: 0.8860 (t80)
REVERT: B  476 CYS cc_start: 0.9194 (m) cc_final: 0.8985 (m)
REVERT: B  513 GLU cc_start: 0.8297 (tp30) cc_final: 0.7830 (tp30)
REVERT: B  521 MET cc_start: 0.8497 (ttp) cc_final: 0.8241 (ttt)
REVERT: B  579 THR cc_start: 0.9516 (p) cc_final: 0.9231 (p)
REVERT: B  582 GLN cc_start: 0.9431 (mt0) cc_final: 0.9048 (mt0)
REVERT: B  592 MET cc_start: 0.9570 (mmm) cc_final: 0.9242 (tpp)
REVERT: B  597 ASP cc_start: 0.9313 (m-30) cc_final: 0.9110 (t0)
REVERT: B  649 TRP cc_start: 0.8003 (t-100) cc_final: 0.7621 (t-100)
REVERT: B  727 LYS cc_start: 0.8003 (mttt) cc_final: 0.7735 (mmtt)
REVERT: B  770 LEU cc_start: 0.8957 (mt) cc_final: 0.8699 (mt)
REVERT: B  785 HIS cc_start: 0.7320 (t-90) cc_final: 0.7106 (t-90)
  outliers start: 0
  outliers final: 0
  residues processed: 236
  average time/residue: 0.0978
  time to fit residues: 36.2018
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  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 155 optimal weight:    2.9990
   chunk 58 optimal weight:    9.9990
   chunk 42 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 136 optimal weight:    7.9990
   chunk 50 optimal weight:    8.9990
   chunk 74 optimal weight:    0.7980
   chunk 35 optimal weight:    0.3980
   chunk 75 optimal weight:    4.9990
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 756 HIS
** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 378 ASN
** B 785 HIS ** 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 = 0.3823 r_free = 0.3823 target = 0.101728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.079310 restraints weight = 48443.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.081643 restraints weight = 35729.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.083415 restraints weight = 28003.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.084788 restraints weight = 23077.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.085843 restraints weight = 19732.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.9443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  13242  Z= 0.159
  Angle     :  0.691  13.066  17966  Z= 0.351
  Chirality :  0.046   0.171   1988
  Planarity :  0.005   0.065   2340
  Dihedral  :  4.853  18.492   1812
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 18.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.21), residues: 1690
  helix:  0.38 (0.19), residues: 702
  sheet: -0.78 (0.32), residues: 258
  loop :  0.32 (0.24), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 451 
 TYR   0.016   0.002   TYR A  38 
 PHE   0.021   0.002   PHE B 311 
 TRP   0.029   0.002   TRP B 733 
 HIS   0.007   0.001   HIS B 785 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (13242)
  covalent geometry    : angle       0.69100 (17966)
  hydrogen bonds       : bond        0.04187 (  602)
  hydrogen bonds       : angle       5.90565 ( 1728)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2582.08 seconds
wall clock time: 45 minutes 39.37 seconds (2739.37 seconds total)