Starting phenix.real_space_refine
on Thu Feb  5 00:47:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wh5_37529/02_2026/8wh5_37529.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wh5_37529/02_2026/8wh5_37529.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wh5_37529/02_2026/8wh5_37529.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wh5_37529/02_2026/8wh5_37529.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wh5_37529/02_2026/8wh5_37529.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wh5_37529/02_2026/8wh5_37529.cif"
  }
  resolution = 3.58
  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=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     P     266      5.49       5
     S      29      5.16       5
     C    8448      2.51       5
     N    2701      2.21       5
     O    3219      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14663
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 766
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 766
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 3, 'TRANS': 90}
    Chain: "B"
      Number of atoms: 617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 617
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 1, 'TRANS': 75}
    Chain: "C"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 662
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 3, 'TRANS': 84}
    Chain: "D"
      Number of atoms: 694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 694
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 3, 'TRANS': 85}
    Chain: "E"
      Number of atoms: 695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 695
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 2, 'TRANS': 82}
    Chain: "F"
      Number of atoms: 706
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 706
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 1, 'TRANS': 85}
    Chain: "G"
      Number of atoms: 750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 750
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "H"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 716
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 3, 'TRANS': 88}
    Chain: "I"
      Number of atoms: 2710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 2710
          Classifications: {'DNA': 133}
          Link IDs: {'rna3p': 132}
    Chain: "J"
      Number of atoms: 2743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 2743
          Classifications: {'DNA': 133}
          Link IDs: {'rna3p': 132}
    Chain: "K"
      Number of atoms: 3604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 445, 3604
          Classifications: {'peptide': 445}
          Link IDs: {'PTRANS': 16, 'TRANS': 428}
          Chain breaks: 1
  Time building chain proxies: 3.23, per 1000 atoms: 0.22
  Number of scatterers: 14663
  At special positions: 0
  Unit cell: (135.09, 135.945, 117.99, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      29     16.00
     P     266     15.00
     O    3219      8.00
     N    2701      7.00
     C    8448      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: 1.21
  Conformation dependent library (CDL) restraints added in 478.5 milliseconds
  

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2156

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 9 sheets defined
      64.7% alpha, 4.1% beta
      103 base pairs and 208 stacking pairs defined.
    Time for finding SS restraints: 2.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.524A  pdb=" N   ARG A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   GLN A  55 " --> pdb=" O   ILE A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.911A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.803A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.793A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.567A  pdb=" N   GLY B  28 " --> pdb=" O   ASN B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.054A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 93
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 38 through 40
      No H-bonds generated for 'chain 'C' and resid 38 through 40'
    Processing helix  chain 'C' and resid 46 through 75
      removed outlier: 4.082A  pdb=" N   VAL C  50 " --> pdb=" O   ALA C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 91
      removed outlier: 3.625A  pdb=" N   ILE C  84 " --> pdb=" O   VAL C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 98
    Processing helix  chain 'D' and resid 62 through 74
    Processing helix  chain 'D' and resid 80 through 108
      removed outlier: 3.521A  pdb=" N   MET D  84 " --> pdb=" O   SER D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 127
      removed outlier: 3.604A  pdb=" N   ILE D 119 " --> pdb=" O   THR D 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 149
      removed outlier: 3.823A  pdb=" N   SER D 137 " --> pdb=" O   LYS D 133 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 55
    Processing helix  chain 'E' and resid 64 through 77
    Processing helix  chain 'E' and resid 87 through 114
      removed outlier: 3.680A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.711A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 40
    Processing helix  chain 'F' and resid 50 through 75
      removed outlier: 4.243A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   VAL F  57 " --> pdb=" O   GLU F  53 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.636A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 27 through 38
    Processing helix  chain 'G' and resid 46 through 75
      removed outlier: 4.423A  pdb=" N   VAL G  50 " --> pdb=" O   ALA G  46 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ARG G  72 " --> pdb=" O   GLY G  68 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ASP G  73 " --> pdb=" O   ASN G  69 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ASN G  74 " --> pdb=" O   ALA G  70 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 91
      removed outlier: 3.512A  pdb=" N   ILE G  84 " --> pdb=" O   VAL G  80 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 98
    Processing helix  chain 'H' and resid 62 through 74
      removed outlier: 3.701A  pdb=" N   LYS H  68 " --> pdb=" O   ILE H  64 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 109
      removed outlier: 4.328A  pdb=" N   SER H  89 " --> pdb=" O   GLY H  85 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 115 through 126
    Processing helix  chain 'H' and resid 129 through 148
      removed outlier: 3.927A  pdb=" N   LYS H 133 " --> pdb=" O   GLY H 129 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 207 through 220
    Processing helix  chain 'K' and resid 233 through 245
      removed outlier: 3.789A  pdb=" N   PHE K 240 " --> pdb=" O   GLN K 236 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   LEU K 241 " --> pdb=" O   THR K 237 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 246 through 249
      removed outlier: 4.175A  pdb=" N   LEU K 249 " --> pdb=" O   GLY K 246 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 246 through 249'
    Processing helix  chain 'K' and resid 258 through 269
    Processing helix  chain 'K' and resid 285 through 294
      removed outlier: 4.216A  pdb=" N   ARG K 292 " --> pdb=" O   ARG K 288 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ARG K 293 " --> pdb=" O   ASP K 289 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 310 through 317
    Processing helix  chain 'K' and resid 317 through 323
      removed outlier: 4.067A  pdb=" N   ILE K 321 " --> pdb=" O   ASP K 317 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ARG K 323 " --> pdb=" O   LYS K 319 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 334 through 339
    Processing helix  chain 'K' and resid 343 through 352
      removed outlier: 3.873A  pdb=" N   HIS K 351 " --> pdb=" O   ARG K 347 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   LEU K 352 " --> pdb=" O   GLU K 348 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 369 through 380
    Processing helix  chain 'K' and resid 416 through 425
      removed outlier: 3.652A  pdb=" N   ILE K 423 " --> pdb=" O   LYS K 419 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 453 through 465
    Processing helix  chain 'K' and resid 467 through 474
      removed outlier: 3.534A  pdb=" N   GLU K 474 " --> pdb=" O   ALA K 470 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 488 through 499
    Processing helix  chain 'K' and resid 500 through 508
    Processing helix  chain 'K' and resid 519 through 522
    Processing helix  chain 'K' and resid 523 through 536
    Processing helix  chain 'K' and resid 550 through 564
      removed outlier: 3.563A  pdb=" N   LYS K 563 " --> pdb=" O   TYR K 559 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 575 through 587
    Processing helix  chain 'K' and resid 604 through 608
      removed outlier: 3.520A  pdb=" N   ILE K 607 " --> pdb=" O   GLY K 604 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ASN K 608 " --> pdb=" O   LEU K 605 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 604 through 608'
    Processing helix  chain 'K' and resid 623 through 635
      removed outlier: 4.322A  pdb=" N   ASP K 627 " --> pdb=" O   ASN K 623 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   CYS K 634 " --> pdb=" O   ALA K 630 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 653 through 674
      removed outlier: 3.654A  pdb=" N   VAL K 672 " --> pdb=" O   LEU K 668 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.379A  pdb=" N   ARG A  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81
    Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 44
      removed outlier: 7.401A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AA5, first strand: chain 'F' and resid 97 through 98
      removed outlier: 3.696A  pdb=" N   TYR F  98 " --> pdb=" O   THR G 102 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'G' and resid 43 through 44
      removed outlier: 7.507A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'K' and resid 278 through 280
      removed outlier: 6.673A  pdb=" N   TYR K 253 " --> pdb=" O   VAL K 307 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   THR K 309 " --> pdb=" O   TYR K 253 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   VAL K 255 " --> pdb=" O   THR K 309 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   LEU K 254 " --> pdb=" O   VAL K 331 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 444 through 450
      removed outlier: 3.587A  pdb=" N   MET K 448 " --> pdb=" O   ARG K 647 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   SER K 649 " --> pdb=" O   MET K 448 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   CYS K 615 " --> pdb=" O   TYR K 646 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   LEU K 648 " --> pdb=" O   CYS K 615 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   LEU K 617 " --> pdb=" O   LEU K 648 " (cutoff:3.500A)
      removed outlier: 9.033A  pdb=" N   THR K 650 " --> pdb=" O   LEU K 617 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   LEU K 544 " --> pdb=" O   ILE K 616 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'K' and resid 568 through 570
      removed outlier: 6.350A  pdb=" N   CYS K 568 " --> pdb=" O   LEU K 597 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    500 hydrogen bonds defined for protein.
    1476 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      269 hydrogen bonds
      530 hydrogen bond angles
      0 basepair planarities
      103 basepair parallelities
      208 stacking parallelities
  Total time for adding SS restraints: 3.26

  Time building geometry restraints manager: 1.62 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 1730
        1.28 -     1.42: 4899
        1.42 -     1.55: 8153
        1.55 -     1.69: 643
        1.69 -     1.82: 48
  Bond restraints: 15473
  Sorted by residual:
  bond pdb=" C   SER K 653 "
       pdb=" O   SER K 653 "
    ideal  model  delta    sigma   weight residual
    1.235  1.315 -0.080 1.02e-02 9.61e+03 6.15e+01
  bond pdb=" C   VAL H 136 "
       pdb=" O   VAL H 136 "
    ideal  model  delta    sigma   weight residual
    1.237  1.148  0.089 1.14e-02 7.69e+03 6.11e+01
  bond pdb=" C   PRO K 258 "
       pdb=" O   PRO K 258 "
    ideal  model  delta    sigma   weight residual
    1.235  1.150  0.085 1.30e-02 5.92e+03 4.30e+01
  bond pdb=" C   ILE K 491 "
       pdb=" O   ILE K 491 "
    ideal  model  delta    sigma   weight residual
    1.237  1.185  0.051 9.80e-03 1.04e+04 2.76e+01
  bond pdb=" CA  SER K 653 "
       pdb=" C   SER K 653 "
    ideal  model  delta    sigma   weight residual
    1.524  1.588 -0.064 1.25e-02 6.40e+03 2.59e+01
  ... (remaining 15468 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.05: 21005
        3.05 -     6.10: 959
        6.10 -     9.16: 51
        9.16 -    12.21: 3
       12.21 -    15.26: 2
  Bond angle restraints: 22020
  Sorted by residual:
  angle pdb=" O3'  DC I 107 "
        pdb=" C3'  DC I 107 "
        pdb=" C2'  DC I 107 "
      ideal   model   delta    sigma   weight residual
     111.50  126.76  -15.26 1.50e+00 4.44e-01 1.04e+02
  angle pdb=" O3'  DG J 112 "
        pdb=" C3'  DG J 112 "
        pdb=" C2'  DG J 112 "
      ideal   model   delta    sigma   weight residual
     111.50  126.00  -14.50 1.50e+00 4.44e-01 9.35e+01
  angle pdb=" N   LYS H 104 "
        pdb=" CA  LYS H 104 "
        pdb=" C   LYS H 104 "
      ideal   model   delta    sigma   weight residual
     111.28  103.00    8.28 1.09e+00 8.42e-01 5.77e+01
  angle pdb=" N   GLU K 518 "
        pdb=" CA  GLU K 518 "
        pdb=" C   GLU K 518 "
      ideal   model   delta    sigma   weight residual
     114.56  104.94    9.62 1.27e+00 6.20e-01 5.74e+01
  angle pdb=" N   ARG D 107 "
        pdb=" CA  ARG D 107 "
        pdb=" C   ARG D 107 "
      ideal   model   delta    sigma   weight residual
     110.97  103.50    7.47 1.09e+00 8.42e-01 4.69e+01
  ... (remaining 22015 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.56: 7380
       35.56 -    71.12: 1198
       71.12 -   106.68: 26
      106.68 -   142.25: 5
      142.25 -   177.81: 5
  Dihedral angle restraints: 8614
    sinusoidal: 5274
      harmonic: 3340
  Sorted by residual:
  dihedral pdb=" CA  VAL B  81 "
           pdb=" C   VAL B  81 "
           pdb=" N   THR B  82 "
           pdb=" CA  THR B  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.34  -22.66     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" C4'  DC I 110 "
           pdb=" C3'  DC I 110 "
           pdb=" O3'  DC I 110 "
           pdb=" P    DC I 111 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   37.81 -177.81     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC I   3 "
           pdb=" C3'  DC I   3 "
           pdb=" O3'  DC I   3 "
           pdb=" P    DG I   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   29.39 -169.39     1      3.50e+01 8.16e-04 1.55e+01
  ... (remaining 8611 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.163: 2433
       0.163 -    0.327: 63
       0.327 -    0.490: 1
       0.490 -    0.654: 0
       0.654 -    0.817: 2
  Chirality restraints: 2499
  Sorted by residual:
  chirality pdb=" C3'  DG J 112 "
            pdb=" C4'  DG J 112 "
            pdb=" O3'  DG J 112 "
            pdb=" C2'  DG J 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -1.84   -0.82 2.00e-01 2.50e+01 1.67e+01
  chirality pdb=" C3'  DC I 107 "
            pdb=" C4'  DC I 107 "
            pdb=" O3'  DC I 107 "
            pdb=" C2'  DC I 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -1.96   -0.70 2.00e-01 2.50e+01 1.24e+01
  chirality pdb=" CA  LEU K 372 "
            pdb=" N   LEU K 372 "
            pdb=" C   LEU K 372 "
            pdb=" CB  LEU K 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.81e+00
  ... (remaining 2496 not shown)

  Planarity restraints: 1858
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER H 148 "    0.024 2.00e-02 2.50e+03   4.70e-02 2.21e+01
        pdb=" C   SER H 148 "   -0.081 2.00e-02 2.50e+03
        pdb=" O   SER H 148 "    0.030 2.00e-02 2.50e+03
        pdb=" N   SER H 149 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU K 376 "    0.021 2.00e-02 2.50e+03   4.38e-02 1.92e+01
        pdb=" C   LEU K 376 "   -0.076 2.00e-02 2.50e+03
        pdb=" O   LEU K 376 "    0.028 2.00e-02 2.50e+03
        pdb=" N   ASN K 377 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  85 "    0.021 2.00e-02 2.50e+03   4.05e-02 1.64e+01
        pdb=" C   GLN A  85 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   GLN A  85 "    0.025 2.00e-02 2.50e+03
        pdb=" N   SER A  86 "    0.024 2.00e-02 2.50e+03
  ... (remaining 1855 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 2326
        2.76 -     3.29: 14097
        3.29 -     3.83: 25940
        3.83 -     4.36: 32559
        4.36 -     4.90: 45781
  Nonbonded interactions: 120703
  Sorted by model distance:
  nonbonded pdb=" O   SER K 620 "
            pdb=" OD1 ASP K 621 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OD2 ASP K 621 "
            pdb=" OD1 ASP K 627 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OD1 ASN K 368 "
            pdb=" N   SER K 370 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" O   LYS K 294 "
            pdb=" NZ  LYS K 294 "
     model   vdw
     2.325 3.120
  nonbonded pdb=" O   GLU G  92 "
            pdb=" OG  SER G  95 "
     model   vdw
     2.351 3.040
  ... (remaining 120698 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 50 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 25 through 100)
  selection = (chain 'F' and resid 25 through 100)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 21 through 108)
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 61 through 149)
}

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:             1.160
  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:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     16.280
  Find NCS groups from input model:        0.130
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
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   0.089  15473  Z= 0.789
  Angle     :  1.348  15.260  22020  Z= 0.953
  Chirality :  0.070   0.817   2499
  Planarity :  0.008   0.047   1858
  Dihedral  : 25.452 177.808   6458
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  :  7.39 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  6.30 %
    Favored  : 92.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -3.46 (0.21), residues: 1136
  helix: -1.56 (0.17), residues: 691
  sheet: -3.21 (0.55), residues: 55
  loop : -3.36 (0.26), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K 431 
 TYR   0.041   0.003   TYR K 329 
 PHE   0.028   0.003   PHE D  67 
 TRP   0.015   0.002   TRP K 482 
 HIS   0.015   0.002   HIS H  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.01210 (15473)
  covalent geometry    : angle       1.34762 (22020)
  hydrogen bonds       : bond        0.22449 (  769)
  hydrogen bonds       : angle       9.65229 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 328
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ILE cc_start: 0.8930 (pt) cc_final: 0.8556 (mt)
REVERT: A   73 GLU cc_start: 0.8019 (tt0) cc_final: 0.7759 (tt0)
REVERT: B   25 ASN cc_start: 0.5358 (m110) cc_final: 0.4649 (m-40)
REVERT: D   81 SER cc_start: 0.8822 (t) cc_final: 0.8573 (p)
REVERT: E   97 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7158 (mt-10)
REVERT: E  123 ASP cc_start: 0.8469 (m-30) cc_final: 0.8235 (m-30)
REVERT: G   74 ASN cc_start: 0.8122 (t0) cc_final: 0.7855 (t0)
REVERT: K  373 TRP cc_start: 0.5573 (t60) cc_final: 0.5303 (t-100)
REVERT: K  432 MET cc_start: 0.8212 (mmm) cc_final: 0.7497 (ttm)
REVERT: K  615 CYS cc_start: 0.7641 (m) cc_final: 0.7156 (m)
REVERT: K  631 MET cc_start: 0.9284 (mtp) cc_final: 0.9074 (mtp)
  outliers start: 9
  outliers final: 0
  residues processed: 334
  average time/residue: 0.1822
  time to fit residues: 80.1219
Evaluate side-chains
  171 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
D  72 GLN
G  90 ASN
G 105 ASN
G 111 ASN
K 629 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.092469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.064651 restraints weight = 50019.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.066464 restraints weight = 27234.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.066896 restraints weight = 16885.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.067179 restraints weight = 15681.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.067165 restraints weight = 14556.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.4052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  15473  Z= 0.257
  Angle     :  0.744  11.428  22020  Z= 0.425
  Chirality :  0.043   0.241   2499
  Planarity :  0.005   0.051   1858
  Dihedral  : 29.296 168.141   4149
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.11 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 14.94 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -0.58 (0.25), residues: 1136
  helix:  1.04 (0.20), residues: 699
  sheet: -2.60 (0.60), residues: 51
  loop : -2.84 (0.27), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  30 
 TYR   0.017   0.002   TYR C  51 
 PHE   0.024   0.002   PHE E  67 
 TRP   0.016   0.002   TRP K 212 
 HIS   0.008   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00585 (15473)
  covalent geometry    : angle       0.74402 (22020)
  hydrogen bonds       : bond        0.07634 (  769)
  hydrogen bonds       : angle       4.03420 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 177
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ILE cc_start: 0.9469 (mm) cc_final: 0.9201 (mt)
REVERT: C  105 ASN cc_start: 0.8225 (t0) cc_final: 0.7818 (t0)
REVERT: G   74 ASN cc_start: 0.8175 (t0) cc_final: 0.7862 (t0)
REVERT: G   93 GLU cc_start: 0.8419 (mp0) cc_final: 0.7893 (mt-10)
REVERT: H  101 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7721 (mm-30)
REVERT: K  265 TRP cc_start: 0.8424 (m100) cc_final: 0.8137 (m-10)
REVERT: K  315 MET cc_start: 0.8305 (tmm) cc_final: 0.8095 (tmm)
REVERT: K  333 ASP cc_start: 0.7508 (t0) cc_final: 0.7240 (t0)
  outliers start: 29
  outliers final: 15
  residues processed: 197
  average time/residue: 0.1254
  time to fit residues: 36.2511
Evaluate side-chains
  158 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  100 ASP
Chi-restraints excluded: chain G residue  111 ASN
Chi-restraints excluded: chain K residue  336 HIS
Chi-restraints excluded: chain K residue  512 LEU
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  609 LEU
Chi-restraints excluded: chain K residue  668 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 122 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    0.8980
   chunk 87 optimal weight:    8.9990
   chunk 85 optimal weight:   10.0000
   chunk 111 optimal weight:    6.9990
   chunk 84 optimal weight:    6.9990
   chunk 116 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 130 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    3.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
C  90 ASN
D 134 HIS
E  85 GLN
F  75 HIS
** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 487 ASN ** 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 = 0.3733 r_free = 0.3733 target = 0.089529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.061555 restraints weight = 50479.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.063194 restraints weight = 27641.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.063773 restraints weight = 17279.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.064020 restraints weight = 15633.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.064053 restraints weight = 14564.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.5237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  15473  Z= 0.231
  Angle     :  0.659   9.729  22020  Z= 0.380
  Chirality :  0.039   0.219   2499
  Planarity :  0.005   0.050   1858
  Dihedral  : 29.161 179.022   4149
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.11 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 15.85 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.39 (0.26), residues: 1136
  helix:  1.84 (0.20), residues: 702
  sheet: -2.04 (0.62), residues: 65
  loop : -2.56 (0.28), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 134 
 TYR   0.019   0.002   TYR K 618 
 PHE   0.015   0.002   PHE D  67 
 TRP   0.012   0.002   TRP K 265 
 HIS   0.008   0.001   HIS G 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 (15473)
  covalent geometry    : angle       0.65929 (22020)
  hydrogen bonds       : bond        0.06878 (  769)
  hydrogen bonds       : angle       3.73408 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 154
  time to evaluate  : 0.487 
Fit side-chains
REVERT: C   90 ASN cc_start: 0.7883 (m-40) cc_final: 0.7554 (m-40)
REVERT: C  105 ASN cc_start: 0.8427 (t0) cc_final: 0.8218 (t0)
REVERT: D  107 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7633 (mtm-85)
REVERT: E   73 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6789 (mt-10)
REVERT: G   74 ASN cc_start: 0.8221 (t0) cc_final: 0.7826 (t0)
REVERT: G   94 LEU cc_start: 0.9078 (mt) cc_final: 0.8726 (mt)
REVERT: H  101 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7539 (mm-30)
REVERT: H  111 LYS cc_start: 0.8219 (mtmt) cc_final: 0.7785 (mmtm)
REVERT: K  333 ASP cc_start: 0.7740 (t0) cc_final: 0.7366 (t0)
REVERT: K  582 GLN cc_start: 0.8772 (mt0) cc_final: 0.8251 (tt0)
  outliers start: 41
  outliers final: 14
  residues processed: 180
  average time/residue: 0.1227
  time to fit residues: 32.6071
Evaluate side-chains
  151 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 136
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain D residue  107 ARG
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  100 ASP
Chi-restraints excluded: chain H residue   66 ILE
Chi-restraints excluded: chain H residue  105 LEU
Chi-restraints excluded: chain K residue  336 HIS
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  609 LEU
Chi-restraints excluded: chain K residue  615 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 104 optimal weight:    6.9990
   chunk 116 optimal weight:    0.0980
   chunk 37 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 109 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 121 optimal weight:    0.0970
   chunk 22 optimal weight:    0.9990
   chunk 69 optimal weight:   10.0000
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
B  93 GLN
F  18 HIS
** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.092299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.064989 restraints weight = 49601.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.066915 restraints weight = 25927.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.067294 restraints weight = 15948.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.067559 restraints weight = 14988.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.067553 restraints weight = 13822.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.5655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15473  Z= 0.151
  Angle     :  0.576   6.653  22020  Z= 0.336
  Chirality :  0.035   0.162   2499
  Planarity :  0.004   0.044   1858
  Dihedral  : 28.812 179.434   4149
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.61 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 17.99 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.11 (0.26), residues: 1136
  helix:  2.34 (0.20), residues: 707
  sheet: -1.44 (0.66), residues: 65
  loop : -2.26 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  82 
 TYR   0.014   0.001   TYR K 511 
 PHE   0.012   0.001   PHE K 240 
 TRP   0.016   0.002   TRP K 265 
 HIS   0.004   0.001   HIS H 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (15473)
  covalent geometry    : angle       0.57565 (22020)
  hydrogen bonds       : bond        0.05287 (  769)
  hydrogen bonds       : angle       3.26287 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 175
  time to evaluate  : 0.450 
Fit side-chains
REVERT: A   76 GLN cc_start: 0.8214 (tp40) cc_final: 0.7879 (tp40)
REVERT: F   20 LYS cc_start: 0.8939 (tppt) cc_final: 0.8736 (mmmt)
REVERT: G   74 ASN cc_start: 0.8108 (t0) cc_final: 0.7648 (t0)
REVERT: H   60 GLU cc_start: 0.8200 (tp30) cc_final: 0.7804 (mm-30)
REVERT: H  101 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7528 (mm-30)
REVERT: H  102 SER cc_start: 0.9075 (t) cc_final: 0.8732 (p)
REVERT: K  333 ASP cc_start: 0.7771 (t0) cc_final: 0.7465 (t0)
REVERT: K  432 MET cc_start: 0.6997 (mmp) cc_final: 0.6093 (tpt)
REVERT: K  501 ASP cc_start: 0.8282 (t0) cc_final: 0.7988 (t0)
REVERT: K  582 GLN cc_start: 0.8693 (mt0) cc_final: 0.8149 (tt0)
  outliers start: 22
  outliers final: 10
  residues processed: 184
  average time/residue: 0.1289
  time to fit residues: 34.3112
Evaluate side-chains
  159 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 149
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  100 ASP
Chi-restraints excluded: chain K residue  317 ASP
Chi-restraints excluded: chain K residue  512 LEU
Chi-restraints excluded: chain K residue  609 LEU
Chi-restraints excluded: chain K residue  615 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 128 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 99 optimal weight:    8.9990
   chunk 93 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0870
   chunk 123 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    2.0166

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
H  88 ASN
K 341 HIS
** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.090373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.062664 restraints weight = 49731.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.064149 restraints weight = 26313.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.064827 restraints weight = 16511.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.064885 restraints weight = 15217.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.064992 restraints weight = 14299.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.5979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  15473  Z= 0.174
  Angle     :  0.581   6.550  22020  Z= 0.339
  Chirality :  0.036   0.143   2499
  Planarity :  0.004   0.042   1858
  Dihedral  : 28.886 179.948   4149
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.75 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.51 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.19 (0.26), residues: 1136
  helix:  2.35 (0.20), residues: 711
  sheet: -1.46 (0.61), residues: 70
  loop : -2.13 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  92 
 TYR   0.010   0.001   TYR C  51 
 PHE   0.008   0.001   PHE B  61 
 TRP   0.013   0.001   TRP K 217 
 HIS   0.003   0.001   HIS K 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (15473)
  covalent geometry    : angle       0.58141 (22020)
  hydrogen bonds       : bond        0.05731 (  769)
  hydrogen bonds       : angle       3.26473 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 140
  time to evaluate  : 0.460 
Fit side-chains
REVERT: C   90 ASN cc_start: 0.7957 (m-40) cc_final: 0.7671 (m-40)
REVERT: C  105 ASN cc_start: 0.8061 (t0) cc_final: 0.7750 (t0)
REVERT: E   52 ARG cc_start: 0.5281 (OUTLIER) cc_final: 0.4448 (mpp-170)
REVERT: G   85 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8339 (tm-30)
REVERT: H   60 GLU cc_start: 0.8162 (tp30) cc_final: 0.7788 (mm-30)
REVERT: H   84 MET cc_start: 0.8611 (mmt) cc_final: 0.8410 (mmt)
REVERT: H  101 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7456 (mm-30)
REVERT: K  333 ASP cc_start: 0.7705 (t0) cc_final: 0.7371 (t0)
REVERT: K  432 MET cc_start: 0.7158 (mmp) cc_final: 0.6218 (mmm)
REVERT: K  501 ASP cc_start: 0.8328 (t0) cc_final: 0.8104 (t0)
REVERT: K  582 GLN cc_start: 0.8746 (mt0) cc_final: 0.8253 (tt0)
  outliers start: 31
  outliers final: 15
  residues processed: 159
  average time/residue: 0.1200
  time to fit residues: 28.5662
Evaluate side-chains
  151 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   79 ILE
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain E residue   52 ARG
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  100 ASP
Chi-restraints excluded: chain K residue  256 ILE
Chi-restraints excluded: chain K residue  336 HIS
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  512 LEU
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  609 LEU
Chi-restraints excluded: chain K residue  615 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 101 optimal weight:   20.0000
   chunk 123 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 39 optimal weight:    0.3980
   chunk 44 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 87 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 74 optimal weight:    7.9990
   chunk 110 optimal weight:    0.9980
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
G 111 ASN
K 295 HIS
** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.089819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.061739 restraints weight = 49138.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.063257 restraints weight = 26116.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.063798 restraints weight = 16536.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.063985 restraints weight = 15770.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.064061 restraints weight = 14473.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.6328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15473  Z= 0.177
  Angle     :  0.584   9.965  22020  Z= 0.339
  Chirality :  0.036   0.148   2499
  Planarity :  0.004   0.041   1858
  Dihedral  : 28.900 179.925   4149
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.23 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 19.61 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.24 (0.26), residues: 1136
  helix:  2.37 (0.20), residues: 708
  sheet: -1.16 (0.63), residues: 68
  loop : -2.10 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K 601 
 TYR   0.013   0.001   TYR G  51 
 PHE   0.008   0.001   PHE K 560 
 TRP   0.015   0.001   TRP K 217 
 HIS   0.003   0.001   HIS K 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (15473)
  covalent geometry    : angle       0.58417 (22020)
  hydrogen bonds       : bond        0.05696 (  769)
  hydrogen bonds       : angle       3.21611 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 0.433 
Fit side-chains
REVERT: C   90 ASN cc_start: 0.7995 (m-40) cc_final: 0.7681 (m-40)
REVERT: C  105 ASN cc_start: 0.8267 (t0) cc_final: 0.8046 (t0)
REVERT: D   96 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7851 (mp0)
REVERT: E   52 ARG cc_start: 0.5296 (OUTLIER) cc_final: 0.4524 (mpp-170)
REVERT: G   85 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8355 (tm-30)
REVERT: H   84 MET cc_start: 0.8644 (mmt) cc_final: 0.8443 (mmt)
REVERT: H  101 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7485 (mm-30)
REVERT: K  333 ASP cc_start: 0.7613 (t0) cc_final: 0.7317 (t0)
REVERT: K  582 GLN cc_start: 0.8793 (mt0) cc_final: 0.8266 (tt0)
  outliers start: 30
  outliers final: 17
  residues processed: 151
  average time/residue: 0.1143
  time to fit residues: 25.9221
Evaluate side-chains
  147 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   96 GLU
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain E residue   52 ARG
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  100 ASP
Chi-restraints excluded: chain G residue  111 ASN
Chi-restraints excluded: chain K residue  256 ILE
Chi-restraints excluded: chain K residue  317 ASP
Chi-restraints excluded: chain K residue  472 LEU
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  512 LEU
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  609 LEU
Chi-restraints excluded: chain K residue  615 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 105 optimal weight:    7.9990
   chunk 45 optimal weight:    0.8980
   chunk 64 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   chunk 116 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 84 optimal weight:    8.9990
   chunk 53 optimal weight:    7.9990
   chunk 69 optimal weight:   10.0000
   chunk 111 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
G 111 ASN
H 134 HIS
** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.089119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.060975 restraints weight = 49535.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.062336 restraints weight = 26933.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.062924 restraints weight = 17198.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.063049 restraints weight = 16496.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.063165 restraints weight = 15055.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.6549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15473  Z= 0.187
  Angle     :  0.593   8.807  22020  Z= 0.341
  Chirality :  0.036   0.175   2499
  Planarity :  0.004   0.052   1858
  Dihedral  : 28.916 179.787   4149
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.75 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 20.53 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.26), residues: 1136
  helix:  2.34 (0.20), residues: 707
  sheet: -1.01 (0.64), residues: 74
  loop : -2.05 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 116 
 TYR   0.011   0.001   TYR C  51 
 PHE   0.008   0.001   PHE B  61 
 TRP   0.016   0.002   TRP K 217 
 HIS   0.010   0.001   HIS D 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (15473)
  covalent geometry    : angle       0.59323 (22020)
  hydrogen bonds       : bond        0.05830 (  769)
  hydrogen bonds       : angle       3.22769 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.482 
Fit side-chains
REVERT: C   90 ASN cc_start: 0.8012 (m-40) cc_final: 0.7681 (m-40)
REVERT: D   96 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7901 (mp0)
REVERT: E   52 ARG cc_start: 0.5258 (OUTLIER) cc_final: 0.4491 (mpp-170)
REVERT: G   85 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8353 (tm-30)
REVERT: H   84 MET cc_start: 0.8651 (mmt) cc_final: 0.8440 (mmt)
REVERT: H  101 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7454 (mm-30)
REVERT: K  333 ASP cc_start: 0.7555 (t0) cc_final: 0.7320 (t0)
REVERT: K  582 GLN cc_start: 0.8809 (mt0) cc_final: 0.8292 (tt0)
  outliers start: 24
  outliers final: 17
  residues processed: 151
  average time/residue: 0.1102
  time to fit residues: 25.2077
Evaluate side-chains
  147 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain D residue   96 GLU
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain E residue   52 ARG
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  100 ASP
Chi-restraints excluded: chain K residue  472 LEU
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  512 LEU
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  609 LEU
Chi-restraints excluded: chain K residue  615 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 48 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 22 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 58 optimal weight:   10.0000
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 111 ASN
H 134 HIS
** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.090312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.062695 restraints weight = 49647.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.064047 restraints weight = 26668.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.064513 restraints weight = 17547.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.064798 restraints weight = 15804.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.064875 restraints weight = 14759.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.6746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15473  Z= 0.159
  Angle     :  0.577   8.790  22020  Z= 0.333
  Chirality :  0.035   0.152   2499
  Planarity :  0.004   0.044   1858
  Dihedral  : 28.791 179.469   4149
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.96 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 21.04 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.40 (0.27), residues: 1136
  helix:  2.45 (0.20), residues: 707
  sheet: -0.73 (0.66), residues: 73
  loop : -2.02 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  30 
 TYR   0.010   0.001   TYR G  51 
 PHE   0.010   0.001   PHE K 560 
 TRP   0.023   0.001   TRP K 217 
 HIS   0.004   0.001   HIS H 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (15473)
  covalent geometry    : angle       0.57654 (22020)
  hydrogen bonds       : bond        0.05254 (  769)
  hydrogen bonds       : angle       3.08207 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 144
  time to evaluate  : 0.394 
Fit side-chains
REVERT: C   90 ASN cc_start: 0.7985 (m-40) cc_final: 0.7677 (m-40)
REVERT: D   96 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7841 (mp0)
REVERT: E   52 ARG cc_start: 0.5271 (OUTLIER) cc_final: 0.4521 (mpp-170)
REVERT: G   85 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8339 (tm-30)
REVERT: H  101 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7451 (mm-30)
REVERT: K  296 MET cc_start: 0.8512 (ptp) cc_final: 0.7787 (pmm)
REVERT: K  333 ASP cc_start: 0.7516 (t0) cc_final: 0.7259 (t0)
REVERT: K  582 GLN cc_start: 0.8784 (mt0) cc_final: 0.8282 (tt0)
  outliers start: 24
  outliers final: 14
  residues processed: 157
  average time/residue: 0.1187
  time to fit residues: 27.8935
Evaluate side-chains
  153 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain D residue   96 GLU
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain E residue   52 ARG
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  100 ASP
Chi-restraints excluded: chain K residue  472 LEU
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  512 LEU
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  609 LEU
Chi-restraints excluded: chain K residue  615 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   chunk 79 optimal weight:   20.0000
   chunk 82 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 100 optimal weight:   10.0000
   chunk 107 optimal weight:   20.0000
   chunk 104 optimal weight:    6.9990
   chunk 73 optimal weight:    7.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 111 ASN
H  72 GLN
H 134 HIS
** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 487 ASN ** 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 = 0.3721 r_free = 0.3721 target = 0.088447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.060334 restraints weight = 49201.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.061546 restraints weight = 26956.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.062117 restraints weight = 17082.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.062326 restraints weight = 15554.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.062463 restraints weight = 14673.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.6893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  15473  Z= 0.210
  Angle     :  0.622   8.040  22020  Z= 0.355
  Chirality :  0.037   0.148   2499
  Planarity :  0.004   0.043   1858
  Dihedral  : 28.850 179.369   4149
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.58 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 22.05 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.14 (0.26), residues: 1136
  helix:  2.23 (0.20), residues: 706
  sheet: -0.74 (0.67), residues: 74
  loop : -2.09 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 117 
 TYR   0.015   0.001   TYR H  62 
 PHE   0.013   0.001   PHE B 100 
 TRP   0.018   0.002   TRP K 217 
 HIS   0.004   0.001   HIS K 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (15473)
  covalent geometry    : angle       0.62213 (22020)
  hydrogen bonds       : bond        0.06302 (  769)
  hydrogen bonds       : angle       3.34566 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  133 GLU cc_start: 0.8423 (mp0) cc_final: 0.8120 (mp0)
REVERT: C   90 ASN cc_start: 0.8006 (m-40) cc_final: 0.7658 (m-40)
REVERT: D   96 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7910 (mp0)
REVERT: E   52 ARG cc_start: 0.5335 (OUTLIER) cc_final: 0.4502 (mpp-170)
REVERT: G   36 LYS cc_start: 0.8969 (tppt) cc_final: 0.8633 (mmtt)
REVERT: G   85 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8387 (tm-30)
REVERT: H  101 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7537 (mm-30)
REVERT: K  296 MET cc_start: 0.8560 (ptp) cc_final: 0.7796 (pmm)
REVERT: K  333 ASP cc_start: 0.7636 (t0) cc_final: 0.7430 (t0)
REVERT: K  582 GLN cc_start: 0.8790 (mt0) cc_final: 0.8319 (tt0)
  outliers start: 23
  outliers final: 18
  residues processed: 150
  average time/residue: 0.1224
  time to fit residues: 27.4934
Evaluate side-chains
  153 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain D residue   96 GLU
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain E residue   52 ARG
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  100 ASP
Chi-restraints excluded: chain G residue  111 ASN
Chi-restraints excluded: chain K residue  472 LEU
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  512 LEU
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  609 LEU
Chi-restraints excluded: chain K residue  615 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 100 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 84 optimal weight:    7.9990
   chunk 78 optimal weight:   10.0000
   chunk 116 optimal weight:   20.0000
   chunk 16 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0670
   overall best weight:    1.7524

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
** K 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 487 ASN ** 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 = 0.3741 r_free = 0.3741 target = 0.089429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.061552 restraints weight = 49202.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.063019 restraints weight = 26159.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.063525 restraints weight = 16778.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.063814 restraints weight = 15843.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.063834 restraints weight = 14687.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.7019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  15473  Z= 0.165
  Angle     :  0.593   8.521  22020  Z= 0.340
  Chirality :  0.035   0.156   2499
  Planarity :  0.004   0.041   1858
  Dihedral  : 28.717 179.715   4149
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.14 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 22.15 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.29 (0.27), residues: 1136
  helix:  2.34 (0.20), residues: 707
  sheet: -0.68 (0.68), residues: 75
  loop : -2.01 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 116 
 TYR   0.010   0.001   TYR H  62 
 PHE   0.007   0.001   PHE B  61 
 TRP   0.022   0.002   TRP K 217 
 HIS   0.003   0.001   HIS G 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (15473)
  covalent geometry    : angle       0.59300 (22020)
  hydrogen bonds       : bond        0.05501 (  769)
  hydrogen bonds       : angle       3.15646 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 GLU cc_start: 0.8399 (mp0) cc_final: 0.8087 (mp0)
REVERT: D   96 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7852 (mp0)
REVERT: E   52 ARG cc_start: 0.5383 (OUTLIER) cc_final: 0.4644 (mpp-170)
REVERT: G   85 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8370 (tm-30)
REVERT: K  296 MET cc_start: 0.8591 (ptp) cc_final: 0.7820 (pmm)
REVERT: K  333 ASP cc_start: 0.7574 (t0) cc_final: 0.7363 (t0)
REVERT: K  582 GLN cc_start: 0.8768 (mt0) cc_final: 0.8241 (tt0)
  outliers start: 21
  outliers final: 17
  residues processed: 153
  average time/residue: 0.1211
  time to fit residues: 27.8495
Evaluate side-chains
  154 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain D residue   96 GLU
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain E residue   52 ARG
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  100 ASP
Chi-restraints excluded: chain K residue  336 HIS
Chi-restraints excluded: chain K residue  472 LEU
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  512 LEU
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  609 LEU
Chi-restraints excluded: chain K residue  615 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 130 optimal weight:   20.0000
   chunk 78 optimal weight:   20.0000
   chunk 34 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 127 optimal weight:    4.9990
   chunk 128 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 104 optimal weight:    7.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
G 111 ASN
** K 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.088552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.060667 restraints weight = 49157.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.061955 restraints weight = 26324.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.062481 restraints weight = 17225.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.062793 restraints weight = 16103.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.062824 restraints weight = 14863.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.7091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15473  Z= 0.195
  Angle     :  0.611   8.752  22020  Z= 0.348
  Chirality :  0.036   0.148   2499
  Planarity :  0.004   0.040   1858
  Dihedral  : 28.713 179.932   4149
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.31 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 21.95 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.23 (0.26), residues: 1136
  helix:  2.23 (0.20), residues: 708
  sheet: -0.51 (0.69), residues: 75
  loop : -1.97 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  95 
 TYR   0.011   0.001   TYR C  51 
 PHE   0.008   0.001   PHE B  61 
 TRP   0.028   0.002   TRP K 217 
 HIS   0.003   0.001   HIS K 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 (15473)
  covalent geometry    : angle       0.61058 (22020)
  hydrogen bonds       : bond        0.05871 (  769)
  hydrogen bonds       : angle       3.25608 ( 2006)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2418.79 seconds
wall clock time: 42 minutes 30.53 seconds (2550.53 seconds total)