Starting phenix.real_space_refine
on Sat Aug 23 06:05:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b5k_44215/08_2025/9b5k_44215.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b5k_44215/08_2025/9b5k_44215.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b5k_44215/08_2025/9b5k_44215.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b5k_44215/08_2025/9b5k_44215.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b5k_44215/08_2025/9b5k_44215.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b5k_44215/08_2025/9b5k_44215.map"
  }
  resolution = 3.16
  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=   0.065
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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      2      5.21       5
     S      43      5.16       5
     C    6449      2.51       5
     N    1678      2.21       5
     O    1953      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10128
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 7734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 985, 7734
          Classifications: {'peptide': 985}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 601
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "C"
      Number of atoms: 1158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1158
          Classifications: {'peptide': 147}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131}
    Chain: "D"
      Number of atoms: 596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 596
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'ATP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Unusual residues: {'A1AIV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.61, per 1000 atoms: 0.26
  Number of scatterers: 10128
  At special positions: 0
  Unit cell: (101.08, 103.208, 120.232, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      43     16.00
     P       3     15.00
     Mg      2     11.99
     O    1953      8.00
     N    1678      7.00
     C    6449      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 593 " - pdb=" SG  CYS C  85 " distance=2.95

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.14
  Conformation dependent library (CDL) restraints added in 460.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2404

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 11 sheets defined
      45.4% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 25
      removed outlier: 3.926A  pdb=" N   TYR A  25 " --> pdb=" O   SER A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 36
    Processing helix  chain 'A' and resid 46 through 60
    Processing helix  chain 'A' and resid 74 through 79
      removed outlier: 3.680A  pdb=" N   SER A  79 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.973A  pdb=" N   ILE A  88 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 101
      removed outlier: 4.233A  pdb=" N   SER A  98 " --> pdb=" O   LYS A  94 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   LYS A  99 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 123
    Processing helix  chain 'A' and resid 132 through 144
      removed outlier: 3.793A  pdb=" N   PHE A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 223
    Processing helix  chain 'A' and resid 267 through 274
      removed outlier: 4.217A  pdb=" N   LYS A 273 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ASP A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 304
      removed outlier: 3.683A  pdb=" N   ILE A 293 " --> pdb=" O   PRO A 289 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLN A 296 " --> pdb=" O   HIS A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 332
    Processing helix  chain 'A' and resid 339 through 349
    Processing helix  chain 'A' and resid 354 through 375
    Processing helix  chain 'A' and resid 389 through 392
    Processing helix  chain 'A' and resid 410 through 418
      removed outlier: 4.625A  pdb=" N   VAL A 416 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 427
    Processing helix  chain 'A' and resid 436 through 450
    Processing helix  chain 'A' and resid 468 through 474
      removed outlier: 3.704A  pdb=" N   ASN A 473 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 483
    Processing helix  chain 'A' and resid 486 through 499
    Processing helix  chain 'A' and resid 500 through 503
    Processing helix  chain 'A' and resid 514 through 518
      removed outlier: 4.086A  pdb=" N   GLU A 518 " --> pdb=" O   PRO A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 527
    Processing helix  chain 'A' and resid 538 through 553
      removed outlier: 3.534A  pdb=" N   ARG A 542 " --> pdb=" O   ASN A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 582
      removed outlier: 3.854A  pdb=" N   SER A 582 " --> pdb=" O   TYR A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 597
    Processing helix  chain 'A' and resid 601 through 618
    Processing helix  chain 'A' and resid 618 through 630
    Processing helix  chain 'A' and resid 632 through 641
      removed outlier: 3.909A  pdb=" N   THR A 636 " --> pdb=" O   ASN A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 656
    Processing helix  chain 'A' and resid 662 through 679
      removed outlier: 3.687A  pdb=" N   CYS A 666 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 689
      removed outlier: 3.576A  pdb=" N   GLN A 683 " --> pdb=" O   ASN A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 737
    Processing helix  chain 'A' and resid 743 through 753
      removed outlier: 3.991A  pdb=" N   TYR A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   GLY A 753 " --> pdb=" O   ARG A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 794
    Processing helix  chain 'A' and resid 796 through 800
    Processing helix  chain 'A' and resid 818 through 835
    Processing helix  chain 'A' and resid 840 through 849
    Processing helix  chain 'A' and resid 855 through 876
      removed outlier: 3.723A  pdb=" N   THR A 859 " --> pdb=" O   MET A 855 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL A 871 " --> pdb=" O   CYS A 867 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   LYS A 872 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 926 through 937
    Processing helix  chain 'A' and resid 958 through 966
    Processing helix  chain 'A' and resid 969 through 979
    Processing helix  chain 'B' and resid 22 through 35
    Processing helix  chain 'B' and resid 37 through 41
    Processing helix  chain 'B' and resid 55 through 60
    Processing helix  chain 'C' and resid 3 through 16
      removed outlier: 3.608A  pdb=" N   ASP C  16 " --> pdb=" O   ASP C  12 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 98 through 112
    Processing helix  chain 'C' and resid 120 through 130
    Processing helix  chain 'C' and resid 130 through 146
    Processing helix  chain 'D' and resid 22 through 35
    Processing helix  chain 'D' and resid 37 through 39
      No H-bonds generated for 'chain 'D' and resid 37 through 39'
    Processing helix  chain 'D' and resid 56 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111
      removed outlier: 6.549A  pdb=" N   ASN A  39 " --> pdb=" O   CYS A 125 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   VAL A 127 " --> pdb=" O   ASN A  39 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   LEU A  41 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   THR A 129 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   ILE A  43 " --> pdb=" O   THR A 129 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   VAL A 126 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   ALA A 153 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   VAL A 128 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   SER A 155 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   TYR A 385 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172
    Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228
      removed outlier: 4.088A  pdb=" N   PHE A 209 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   THR A 195 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   ILE A 188 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   VAL A 193 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228
      removed outlier: 4.088A  pdb=" N   PHE A 209 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509
      removed outlier: 6.579A  pdb=" N   ILE A 459 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   TYR A 509 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   VAL A 461 " --> pdb=" O   TYR A 509 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER A 460 " --> pdb=" O   THR A 430 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   LEU A 531 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   SER A 559 " --> pdb=" O   ASN A 534 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 908
    Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 923
      removed outlier: 6.449A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   VAL A 990 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   SER A 947 " --> pdb=" O   VAL A 990 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   GLU A 992 " --> pdb=" O   LEU A 945 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   LEU A 945 " --> pdb=" O   GLU A 992 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   CYS A 994 " --> pdb=" O   THR A 943 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   SER A 947 " --> pdb=" O   LEU A 951 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   LEU A 951 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 923
      removed outlier: 6.449A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   CYS A 995 " --> pdb=" O   VAL A1003 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 12 through 16
      removed outlier: 3.847A  pdb=" N   ARG B  42 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 26
      removed outlier: 10.644A  pdb=" N   SER C  22 " --> pdb=" O   TRP C  33 " (cutoff:3.500A)
      removed outlier: 9.501A  pdb=" N   TRP C  33 " --> pdb=" O   SER C  22 " (cutoff:3.500A)
      removed outlier: 10.408A  pdb=" N   GLY C  24 " --> pdb=" O   PHE C  31 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   PHE C  31 " --> pdb=" O   GLY C  24 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   VAL C  26 " --> pdb=" O   ASP C  29 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 16

    490 hydrogen bonds defined for protein.
    1323 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.58

  Time building geometry restraints manager: 1.45 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1723
        1.27 -     1.40: 2410
        1.40 -     1.54: 6020
        1.54 -     1.67: 125
        1.67 -     1.81: 66
  Bond restraints: 10344
  Sorted by residual:
  bond pdb=" C04 A1AIV D 101 "
       pdb=" C05 A1AIV D 101 "
    ideal  model  delta    sigma   weight residual
    1.453  1.526 -0.073 2.00e-02 2.50e+03 1.34e+01
  bond pdb=" N   MET B   1 "
       pdb=" CA  MET B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.71e+00
  bond pdb=" N   MET D   1 "
       pdb=" CA  MET D   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.66e+00
  bond pdb=" C05 A1AIV D 101 "
       pdb=" N06 A1AIV D 101 "
    ideal  model  delta    sigma   weight residual
    1.151  1.132  0.019 2.00e-02 2.50e+03 9.10e-01
  bond pdb=" C1' ATP A1103 "
       pdb=" C2' ATP A1103 "
    ideal  model  delta    sigma   weight residual
    1.531  1.520  0.011 1.20e-02 6.94e+03 8.21e-01
  ... (remaining 10339 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 13879
        1.59 -     3.19: 74
        3.19 -     4.78: 50
        4.78 -     6.37: 4
        6.37 -     7.97: 2
  Bond angle restraints: 14009
  Sorted by residual:
  angle pdb=" C   LYS A 381 "
        pdb=" N   GLN A 382 "
        pdb=" CA  GLN A 382 "
      ideal   model   delta    sigma   weight residual
     121.70  128.17   -6.47 1.80e+00 3.09e-01 1.29e+01
  angle pdb=" C03 A1AIV D 101 "
        pdb=" C02 A1AIV D 101 "
        pdb=" N01 A1AIV D 101 "
      ideal   model   delta    sigma   weight residual
     111.06  103.09    7.97 3.00e+00 1.11e-01 7.05e+00
  angle pdb=" C2' ATP A1103 "
        pdb=" C1' ATP A1103 "
        pdb=" O4' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     106.53  103.57    2.96 1.18e+00 7.24e-01 6.36e+00
  angle pdb=" C3' ATP A1103 "
        pdb=" C4' ATP A1103 "
        pdb=" C5' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     115.19  110.79    4.40 1.76e+00 3.23e-01 6.26e+00
  angle pdb=" C2' ATP A1103 "
        pdb=" C3' ATP A1103 "
        pdb=" O3' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     111.83  105.82    6.01 2.67e+00 1.40e-01 5.07e+00
  ... (remaining 14004 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.88: 5984
       14.88 -    29.76: 249
       29.76 -    44.65: 53
       44.65 -    59.53: 17
       59.53 -    74.41: 5
  Dihedral angle restraints: 6308
    sinusoidal: 2587
      harmonic: 3721
  Sorted by residual:
  dihedral pdb=" CB  CYS A 593 "
           pdb=" SG  CYS A 593 "
           pdb=" SG  CYS C  85 "
           pdb=" CB  CYS C  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -136.22   50.22     1      1.00e+01 1.00e-02 3.46e+01
  dihedral pdb=" N   THR C 111 "
           pdb=" CA  THR C 111 "
           pdb=" CB  THR C 111 "
           pdb=" OG1 THR C 111 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.22  -59.78     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   GLU A 869 "
           pdb=" CA  GLU A 869 "
           pdb=" CB  GLU A 869 "
           pdb=" CG  GLU A 869 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.52  -58.48     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 6305 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1357
       0.054 -    0.108: 162
       0.108 -    0.162: 46
       0.162 -    0.216: 0
       0.216 -    0.270: 3
  Chirality restraints: 1568
  Sorted by residual:
  chirality pdb=" C2' ATP A1103 "
            pdb=" C1' ATP A1103 "
            pdb=" C3' ATP A1103 "
            pdb=" O2' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.95    0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" C3' ATP A1103 "
            pdb=" C2' ATP A1103 "
            pdb=" C4' ATP A1103 "
            pdb=" O3' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.89    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" C4' ATP A1103 "
            pdb=" C3' ATP A1103 "
            pdb=" C5' ATP A1103 "
            pdb=" O4' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.73    0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 1565 not shown)

  Planarity restraints: 1812
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  94 "    0.021 5.00e-02 4.00e+02   3.16e-02 1.60e+00
        pdb=" N   PRO C  95 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO C  95 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C  95 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 922 "    0.015 5.00e-02 4.00e+02   2.30e-02 8.47e-01
        pdb=" N   PRO A 923 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO A 923 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 923 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  63 "   -0.014 5.00e-02 4.00e+02   2.16e-02 7.44e-01
        pdb=" N   PRO C  64 "    0.037 5.00e-02 4.00e+02
        pdb=" CA  PRO C  64 "   -0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO C  64 "   -0.012 5.00e-02 4.00e+02
  ... (remaining 1809 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 81
        2.61 -     3.18: 8822
        3.18 -     3.76: 14723
        3.76 -     4.33: 21346
        4.33 -     4.90: 36639
  Nonbonded interactions: 81611
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 465 "
            pdb="MG    MG A1102 "
     model   vdw
     2.039 2.170
  nonbonded pdb="MG    MG A1101 "
            pdb=" O2B ATP A1103 "
     model   vdw
     2.119 2.170
  nonbonded pdb=" OD2 ASP A 537 "
            pdb="MG    MG A1101 "
     model   vdw
     2.122 2.170
  nonbonded pdb=" OD2 ASP A 463 "
            pdb=" O3' ATP A1103 "
     model   vdw
     2.180 3.040
  nonbonded pdb="MG    MG A1101 "
            pdb=" O2A ATP A1103 "
     model   vdw
     2.212 2.170
  ... (remaining 81606 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 'B' and resid 1 through 75)
  selection = (chain 'D' and resid 1 through 75)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.500
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
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      :  0.010   0.920  10347  Z= 0.482
  Angle     :  0.628  50.913  14011  Z= 0.307
  Chirality :  0.042   0.270   1568
  Planarity :  0.003   0.032   1812
  Dihedral  :  9.403  74.412   3901
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  2.74 %
    Favored  : 95.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.24), residues: 1273
  helix:  2.21 (0.24), residues: 491
  sheet:  0.79 (0.35), residues: 209
  loop :  0.45 (0.27), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 965 
 TYR   0.007   0.001   TYR A 509 
 PHE   0.008   0.001   PHE A 842 
 TRP   0.006   0.001   TRP C  93 
 HIS   0.002   0.000   HIS C  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10344)
  covalent geometry    : angle       0.45066 (14009)
  SS BOND              : bond        0.91983 (    1)
  SS BOND              : angle      36.60987 (    2)
  hydrogen bonds       : bond        0.14008 (  477)
  hydrogen bonds       : angle       5.64589 ( 1323)
  Misc. bond           : bond        0.07857 (    2)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 220
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8684 (tp30) cc_final: 0.8315 (tp30)
REVERT: A  184 MET cc_start: 0.8545 (mtm) cc_final: 0.8088 (mtt)
REVERT: A  196 MET cc_start: 0.8288 (mmp) cc_final: 0.7785 (mmm)
REVERT: A  229 VAL cc_start: 0.8916 (t) cc_final: 0.8267 (p)
REVERT: A  413 GLN cc_start: 0.8596 (tt0) cc_final: 0.8371 (tt0)
REVERT: A  465 ASP cc_start: 0.8127 (t0) cc_final: 0.7926 (t0)
REVERT: A  543 MET cc_start: 0.8243 (mmt) cc_final: 0.7934 (mmt)
REVERT: A  645 ARG cc_start: 0.9096 (ptm-80) cc_final: 0.8809 (tpp80)
REVERT: A  915 LYS cc_start: 0.8798 (tppt) cc_final: 0.8589 (ttpp)
REVERT: A  925 CYS cc_start: 0.8079 (p) cc_final: 0.7831 (p)
REVERT: A  944 MET cc_start: 0.8046 (tmt) cc_final: 0.7325 (tmm)
REVERT: A  987 LYS cc_start: 0.8929 (mtpt) cc_final: 0.8405 (mmtt)
REVERT: B   11 LYS cc_start: 0.8509 (tttt) cc_final: 0.8196 (ttpt)
REVERT: C   59 ASP cc_start: 0.8905 (t0) cc_final: 0.8597 (t0)
REVERT: C   93 TRP cc_start: 0.5841 (OUTLIER) cc_final: 0.3147 (t-100)
REVERT: C  116 ASP cc_start: 0.8003 (m-30) cc_final: 0.7520 (m-30)
REVERT: C  117 ASP cc_start: 0.8184 (t0) cc_final: 0.7838 (m-30)
REVERT: C  127 TYR cc_start: 0.8293 (t80) cc_final: 0.8090 (t80)
  outliers start: 15
  outliers final: 7
  residues processed: 230
  average time/residue: 0.1272
  time to fit residues: 37.9287
Evaluate side-chains
  135 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 127
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue   93 TRP
Chi-restraints excluded: chain C residue  111 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 123 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.110206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.076975 restraints weight = 18292.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 3.30
r_work: 0.2976 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082  10347  Z= 0.131
  Angle     :  0.533   8.345  14011  Z= 0.273
  Chirality :  0.043   0.171   1568
  Planarity :  0.004   0.045   1812
  Dihedral  :  6.696  89.562   1421
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  6.46 %
    Favored  : 91.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.24), residues: 1273
  helix:  1.94 (0.24), residues: 510
  sheet:  0.92 (0.35), residues: 213
  loop :  0.45 (0.28), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  73 
 TYR   0.013   0.001   TYR C  74 
 PHE   0.010   0.001   PHE A 842 
 TRP   0.009   0.001   TRP C  93 
 HIS   0.002   0.000   HIS A 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (10344)
  covalent geometry    : angle       0.52945 (14009)
  SS BOND              : bond        0.01902 (    1)
  SS BOND              : angle       5.08960 (    2)
  hydrogen bonds       : bond        0.03943 (  477)
  hydrogen bonds       : angle       4.56434 ( 1323)
  Misc. bond           : bond        0.00385 (    2)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8680 (tp30) cc_final: 0.8297 (tp30)
REVERT: A  184 MET cc_start: 0.8684 (mtm) cc_final: 0.8332 (mtt)
REVERT: A  185 ILE cc_start: 0.8682 (mt) cc_final: 0.8415 (mp)
REVERT: A  196 MET cc_start: 0.8384 (mmp) cc_final: 0.8172 (mmt)
REVERT: A  205 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7485 (mt-10)
REVERT: A  229 VAL cc_start: 0.8941 (t) cc_final: 0.8572 (p)
REVERT: A  465 ASP cc_start: 0.8333 (t0) cc_final: 0.8035 (t0)
REVERT: A  626 MET cc_start: 0.8757 (tpp) cc_final: 0.8406 (tpt)
REVERT: A  645 ARG cc_start: 0.9155 (ptm-80) cc_final: 0.8798 (tpt-90)
REVERT: A  915 LYS cc_start: 0.8833 (tppt) cc_final: 0.8584 (ttpp)
REVERT: A  925 CYS cc_start: 0.8253 (p) cc_final: 0.8013 (p)
REVERT: A  987 LYS cc_start: 0.8958 (mtpt) cc_final: 0.8397 (mmtt)
REVERT: B   11 LYS cc_start: 0.8440 (tttt) cc_final: 0.8237 (ttpp)
REVERT: B   60 ASN cc_start: 0.8283 (t0) cc_final: 0.7831 (t0)
REVERT: C   59 ASP cc_start: 0.8731 (t0) cc_final: 0.8405 (t0)
REVERT: C  143 ARG cc_start: 0.8750 (ttp80) cc_final: 0.8319 (mtm110)
  outliers start: 18
  outliers final: 13
  residues processed: 153
  average time/residue: 0.1260
  time to fit residues: 26.2301
Evaluate side-chains
  134 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  926 THR
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain D residue   22 THR
Chi-restraints excluded: chain D residue   56 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 91 optimal weight:    0.4980
   chunk 40 optimal weight:    0.8980
   chunk 99 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 121 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.8784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.114823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.081465 restraints weight = 17279.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 3.33
r_work: 0.2973 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10347  Z= 0.140
  Angle     :  0.498   8.286  14011  Z= 0.255
  Chirality :  0.042   0.150   1568
  Planarity :  0.004   0.044   1812
  Dihedral  :  6.491  77.133   1416
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  7.61 %
    Favored  : 90.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.24), residues: 1273
  helix:  1.85 (0.23), residues: 514
  sheet:  0.95 (0.35), residues: 213
  loop :  0.36 (0.28), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 841 
 TYR   0.017   0.001   TYR C  60 
 PHE   0.008   0.001   PHE C  62 
 TRP   0.009   0.001   TRP C  93 
 HIS   0.002   0.000   HIS C  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (10344)
  covalent geometry    : angle       0.49595 (14009)
  SS BOND              : bond        0.01013 (    1)
  SS BOND              : angle       4.04055 (    2)
  hydrogen bonds       : bond        0.03682 (  477)
  hydrogen bonds       : angle       4.41635 ( 1323)
  Misc. bond           : bond        0.00203 (    2)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8606 (tp30) cc_final: 0.8194 (tp30)
REVERT: A  184 MET cc_start: 0.8527 (mtm) cc_final: 0.8182 (mtt)
REVERT: A  196 MET cc_start: 0.8144 (mmp) cc_final: 0.7866 (mmt)
REVERT: A  205 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7222 (mt-10)
REVERT: A  229 VAL cc_start: 0.8684 (t) cc_final: 0.8300 (p)
REVERT: A  334 PHE cc_start: 0.7556 (m-80) cc_final: 0.7260 (m-10)
REVERT: A  465 ASP cc_start: 0.8134 (t0) cc_final: 0.7735 (t0)
REVERT: A  626 MET cc_start: 0.8623 (tpp) cc_final: 0.8284 (tpt)
REVERT: A  645 ARG cc_start: 0.9146 (ptm-80) cc_final: 0.8757 (tpt-90)
REVERT: A  719 ARG cc_start: 0.7881 (mmm160) cc_final: 0.7613 (mmm160)
REVERT: A  915 LYS cc_start: 0.8593 (tppt) cc_final: 0.8353 (ttpp)
REVERT: A  925 CYS cc_start: 0.8198 (p) cc_final: 0.7951 (p)
REVERT: A  987 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8147 (mmtt)
REVERT: B   60 ASN cc_start: 0.8253 (t0) cc_final: 0.7698 (t0)
REVERT: B   64 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8791 (mm-30)
REVERT: C   59 ASP cc_start: 0.8587 (t0) cc_final: 0.8106 (t0)
REVERT: C   93 TRP cc_start: 0.5927 (OUTLIER) cc_final: 0.3436 (t-100)
REVERT: C  143 ARG cc_start: 0.8702 (ttp80) cc_final: 0.8236 (ttp-110)
  outliers start: 23
  outliers final: 18
  residues processed: 142
  average time/residue: 0.1020
  time to fit residues: 20.0130
Evaluate side-chains
  136 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  855 MET
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  926 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue   93 TRP
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain D residue   22 THR
Chi-restraints excluded: chain D residue   56 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 104 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9990
   chunk 120 optimal weight:    8.9990
   overall best weight:    1.2386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.113361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.079789 restraints weight = 17650.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 3.37
r_work: 0.2943 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10347  Z= 0.177
  Angle     :  0.519   8.243  14011  Z= 0.266
  Chirality :  0.043   0.170   1568
  Planarity :  0.004   0.045   1812
  Dihedral  :  6.676  79.064   1416
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  :  7.61 %
    Favored  : 89.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.24), residues: 1273
  helix:  1.71 (0.23), residues: 515
  sheet:  0.96 (0.35), residues: 210
  loop :  0.23 (0.27), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 841 
 TYR   0.019   0.001   TYR C 127 
 PHE   0.020   0.001   PHE C  62 
 TRP   0.011   0.001   TRP C  93 
 HIS   0.002   0.001   HIS A 604 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (10344)
  covalent geometry    : angle       0.51652 (14009)
  SS BOND              : bond        0.01229 (    1)
  SS BOND              : angle       4.09053 (    2)
  hydrogen bonds       : bond        0.03852 (  477)
  hydrogen bonds       : angle       4.41567 ( 1323)
  Misc. bond           : bond        0.00068 (    2)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 124
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8606 (tp30) cc_final: 0.8181 (tp30)
REVERT: A  184 MET cc_start: 0.8553 (mtm) cc_final: 0.8151 (mtt)
REVERT: A  185 ILE cc_start: 0.8695 (mt) cc_final: 0.8359 (mp)
REVERT: A  196 MET cc_start: 0.8090 (mmp) cc_final: 0.7822 (mmt)
REVERT: A  334 PHE cc_start: 0.7574 (m-80) cc_final: 0.7296 (m-10)
REVERT: A  442 MET cc_start: 0.7477 (tpp) cc_final: 0.6875 (mmm)
REVERT: A  546 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8170 (t0)
REVERT: A  567 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8477 (p0)
REVERT: A  645 ARG cc_start: 0.9162 (ptm-80) cc_final: 0.8810 (tpt-90)
REVERT: A  719 ARG cc_start: 0.7984 (mmm160) cc_final: 0.7679 (mmm160)
REVERT: A  915 LYS cc_start: 0.8597 (ttpt) cc_final: 0.8384 (ttpp)
REVERT: A  987 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8260 (mttm)
REVERT: B   51 GLU cc_start: 0.8244 (mt-10) cc_final: 0.8011 (mt-10)
REVERT: B   60 ASN cc_start: 0.8327 (t0) cc_final: 0.7741 (t0)
REVERT: C   59 ASP cc_start: 0.8667 (t0) cc_final: 0.8285 (t0)
REVERT: C   93 TRP cc_start: 0.6049 (OUTLIER) cc_final: 0.3674 (t-100)
REVERT: D   41 GLN cc_start: 0.7010 (mt0) cc_final: 0.6311 (mp10)
REVERT: D   59 TYR cc_start: 0.8305 (m-80) cc_final: 0.8021 (m-80)
  outliers start: 34
  outliers final: 24
  residues processed: 147
  average time/residue: 0.0914
  time to fit residues: 18.7877
Evaluate side-chains
  143 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  546 ASP
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  567 ASN
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  926 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue   93 TRP
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   70 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 81 optimal weight:    0.0010
   chunk 50 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 71 optimal weight:    0.5980
   chunk 58 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 75 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.6386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.114373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.081103 restraints weight = 17392.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 3.34
r_work: 0.2970 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10347  Z= 0.112
  Angle     :  0.477   7.075  14011  Z= 0.244
  Chirality :  0.041   0.164   1568
  Planarity :  0.004   0.043   1812
  Dihedral  :  6.480  80.009   1416
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  :  9.20 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.24), residues: 1273
  helix:  1.76 (0.23), residues: 515
  sheet:  0.98 (0.35), residues: 218
  loop :  0.24 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 841 
 TYR   0.022   0.001   TYR C 134 
 PHE   0.025   0.001   PHE C  62 
 TRP   0.009   0.001   TRP C  93 
 HIS   0.002   0.000   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (10344)
  covalent geometry    : angle       0.47494 (14009)
  SS BOND              : bond        0.00633 (    1)
  SS BOND              : angle       3.66147 (    2)
  hydrogen bonds       : bond        0.03374 (  477)
  hydrogen bonds       : angle       4.28395 ( 1323)
  Misc. bond           : bond        0.00045 (    2)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8591 (tp30) cc_final: 0.8189 (tp30)
REVERT: A  184 MET cc_start: 0.8419 (mtm) cc_final: 0.7812 (mtt)
REVERT: A  185 ILE cc_start: 0.8691 (mt) cc_final: 0.8330 (mp)
REVERT: A  196 MET cc_start: 0.8068 (mmp) cc_final: 0.7758 (mmt)
REVERT: A  334 PHE cc_start: 0.7552 (m-80) cc_final: 0.7279 (m-10)
REVERT: A  546 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8134 (t0)
REVERT: A  645 ARG cc_start: 0.9166 (ptm-80) cc_final: 0.8816 (tpt-90)
REVERT: A  915 LYS cc_start: 0.8639 (ttpt) cc_final: 0.8402 (ttpp)
REVERT: A  987 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8119 (mmtt)
REVERT: B   60 ASN cc_start: 0.8346 (t0) cc_final: 0.7753 (t0)
REVERT: B   64 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8770 (mm-30)
REVERT: C   59 ASP cc_start: 0.8560 (t0) cc_final: 0.7760 (t70)
REVERT: C   93 TRP cc_start: 0.6113 (OUTLIER) cc_final: 0.3938 (t-100)
REVERT: D   41 GLN cc_start: 0.7055 (mt0) cc_final: 0.6352 (mp10)
REVERT: D   59 TYR cc_start: 0.8396 (m-80) cc_final: 0.8047 (m-80)
  outliers start: 28
  outliers final: 20
  residues processed: 140
  average time/residue: 0.1144
  time to fit residues: 21.5626
Evaluate side-chains
  138 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 116
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  498 MET
Chi-restraints excluded: chain A residue  546 ASP
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue   93 TRP
Chi-restraints excluded: chain D residue   22 THR
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   70 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 115 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 82 optimal weight:    0.7980
   chunk 113 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 86 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.114126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.080801 restraints weight = 17483.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 3.35
r_work: 0.2967 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10347  Z= 0.123
  Angle     :  0.473   6.795  14011  Z= 0.243
  Chirality :  0.041   0.169   1568
  Planarity :  0.004   0.042   1812
  Dihedral  :  6.442  81.536   1415
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  :  8.94 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.24), residues: 1273
  helix:  1.76 (0.23), residues: 515
  sheet:  0.99 (0.35), residues: 218
  loop :  0.24 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 143 
 TYR   0.015   0.001   TYR C 127 
 PHE   0.012   0.001   PHE C  62 
 TRP   0.009   0.001   TRP C  93 
 HIS   0.002   0.000   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10344)
  covalent geometry    : angle       0.47149 (14009)
  SS BOND              : bond        0.00911 (    1)
  SS BOND              : angle       3.38426 (    2)
  hydrogen bonds       : bond        0.03355 (  477)
  hydrogen bonds       : angle       4.22729 ( 1323)
  Misc. bond           : bond        0.00122 (    2)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 120
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8594 (tp30) cc_final: 0.8181 (tp30)
REVERT: A  184 MET cc_start: 0.8410 (mtm) cc_final: 0.7810 (mtt)
REVERT: A  185 ILE cc_start: 0.8611 (mt) cc_final: 0.8257 (mp)
REVERT: A  196 MET cc_start: 0.8035 (mmp) cc_final: 0.7740 (mmt)
REVERT: A  334 PHE cc_start: 0.7552 (m-80) cc_final: 0.7263 (m-10)
REVERT: A  442 MET cc_start: 0.7512 (tpp) cc_final: 0.6891 (mmm)
REVERT: A  465 ASP cc_start: 0.8129 (t0) cc_final: 0.7610 (t0)
REVERT: A  546 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8168 (t0)
REVERT: A  567 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8483 (p0)
REVERT: A  645 ARG cc_start: 0.9162 (ptm-80) cc_final: 0.8816 (tpt-90)
REVERT: A  719 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7598 (mmm160)
REVERT: A  915 LYS cc_start: 0.8653 (ttpt) cc_final: 0.8404 (ttpp)
REVERT: A  987 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8295 (mttm)
REVERT: B   60 ASN cc_start: 0.8369 (t0) cc_final: 0.7797 (t0)
REVERT: B   64 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8773 (mm-30)
REVERT: C   38 MET cc_start: 0.8336 (mtm) cc_final: 0.8042 (ptp)
REVERT: C   59 ASP cc_start: 0.8561 (t0) cc_final: 0.7774 (t70)
REVERT: C   93 TRP cc_start: 0.6097 (OUTLIER) cc_final: 0.3910 (t-100)
REVERT: C  143 ARG cc_start: 0.8756 (ttp80) cc_final: 0.8331 (mtm110)
REVERT: D   41 GLN cc_start: 0.6987 (mt0) cc_final: 0.6379 (mp10)
REVERT: D   59 TYR cc_start: 0.8461 (m-80) cc_final: 0.8104 (m-80)
  outliers start: 31
  outliers final: 24
  residues processed: 140
  average time/residue: 0.0873
  time to fit residues: 16.9756
Evaluate side-chains
  143 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  498 MET
Chi-restraints excluded: chain A residue  546 ASP
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  567 ASN
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  588 LYS
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  926 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue   93 TRP
Chi-restraints excluded: chain D residue   22 THR
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   70 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 78 optimal weight:    0.0030
   chunk 6 optimal weight:    0.1980
   chunk 91 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0570
   chunk 74 optimal weight:    7.9990
   overall best weight:    0.4308

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.115386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.082145 restraints weight = 17261.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 3.34
r_work: 0.2986 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10347  Z= 0.093
  Angle     :  0.456   6.156  14011  Z= 0.233
  Chirality :  0.041   0.144   1568
  Planarity :  0.004   0.041   1812
  Dihedral  :  6.356  83.481   1415
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  :  9.65 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.24), residues: 1273
  helix:  1.84 (0.23), residues: 515
  sheet:  1.15 (0.35), residues: 205
  loop :  0.27 (0.27), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 841 
 TYR   0.013   0.001   TYR C 127 
 PHE   0.008   0.001   PHE A 724 
 TRP   0.009   0.001   TRP C  93 
 HIS   0.001   0.000   HIS C  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 (10344)
  covalent geometry    : angle       0.45482 (14009)
  SS BOND              : bond        0.00451 (    1)
  SS BOND              : angle       3.07299 (    2)
  hydrogen bonds       : bond        0.03032 (  477)
  hydrogen bonds       : angle       4.12853 ( 1323)
  Misc. bond           : bond        0.00073 (    2)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8571 (tp30) cc_final: 0.8152 (tp30)
REVERT: A  184 MET cc_start: 0.8393 (mtm) cc_final: 0.8079 (mtt)
REVERT: A  185 ILE cc_start: 0.8602 (mt) cc_final: 0.8277 (mp)
REVERT: A  334 PHE cc_start: 0.7514 (m-80) cc_final: 0.7212 (m-10)
REVERT: A  442 MET cc_start: 0.7473 (tpp) cc_final: 0.6878 (mmm)
REVERT: A  465 ASP cc_start: 0.8111 (t0) cc_final: 0.7593 (t0)
REVERT: A  546 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8119 (t0)
REVERT: A  567 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8456 (p0)
REVERT: A  645 ARG cc_start: 0.9133 (ptm-80) cc_final: 0.8791 (tpt-90)
REVERT: A  658 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8042 (mp0)
REVERT: A  719 ARG cc_start: 0.7986 (mmm160) cc_final: 0.7537 (mmm160)
REVERT: A  987 LYS cc_start: 0.8835 (mtpt) cc_final: 0.8296 (mttm)
REVERT: B   60 ASN cc_start: 0.8389 (t0) cc_final: 0.7840 (t0)
REVERT: B   64 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8735 (mm-30)
REVERT: C   38 MET cc_start: 0.8334 (mtm) cc_final: 0.8002 (ptp)
REVERT: C   59 ASP cc_start: 0.8550 (t0) cc_final: 0.7736 (t70)
REVERT: C   93 TRP cc_start: 0.6116 (OUTLIER) cc_final: 0.3985 (t-100)
REVERT: C  116 ASP cc_start: 0.7685 (m-30) cc_final: 0.6937 (t0)
REVERT: C  131 ARG cc_start: 0.8349 (mmm-85) cc_final: 0.8072 (mmm-85)
REVERT: C  143 ARG cc_start: 0.8750 (ttp80) cc_final: 0.8236 (ttp-110)
REVERT: D   41 GLN cc_start: 0.7034 (mt0) cc_final: 0.6367 (mp10)
REVERT: D   59 TYR cc_start: 0.8374 (m-80) cc_final: 0.7992 (m-80)
  outliers start: 25
  outliers final: 21
  residues processed: 138
  average time/residue: 0.1023
  time to fit residues: 19.4765
Evaluate side-chains
  140 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  498 MET
Chi-restraints excluded: chain A residue  546 ASP
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  567 ASN
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  926 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue   93 TRP
Chi-restraints excluded: chain D residue   22 THR
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   70 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   chunk 106 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 117 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   chunk 102 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.114173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.080915 restraints weight = 17440.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 3.34
r_work: 0.2964 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10347  Z= 0.125
  Angle     :  0.480   8.208  14011  Z= 0.244
  Chirality :  0.041   0.141   1568
  Planarity :  0.004   0.039   1812
  Dihedral  :  6.419  87.035   1415
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  :  9.12 %
    Favored  : 88.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.24), residues: 1273
  helix:  1.83 (0.23), residues: 516
  sheet:  1.14 (0.35), residues: 205
  loop :  0.25 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 841 
 TYR   0.026   0.001   TYR C  60 
 PHE   0.009   0.001   PHE A 431 
 TRP   0.009   0.001   TRP C  93 
 HIS   0.002   0.000   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10344)
  covalent geometry    : angle       0.47816 (14009)
  SS BOND              : bond        0.00519 (    1)
  SS BOND              : angle       3.21087 (    2)
  hydrogen bonds       : bond        0.03264 (  477)
  hydrogen bonds       : angle       4.14376 ( 1323)
  Misc. bond           : bond        0.00092 (    2)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 116
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8583 (tp30) cc_final: 0.7971 (tp30)
REVERT: A  184 MET cc_start: 0.8268 (mtm) cc_final: 0.7927 (mtt)
REVERT: A  185 ILE cc_start: 0.8552 (mt) cc_final: 0.8269 (mp)
REVERT: A  334 PHE cc_start: 0.7525 (m-80) cc_final: 0.7222 (m-10)
REVERT: A  442 MET cc_start: 0.7539 (tpp) cc_final: 0.6955 (mmm)
REVERT: A  465 ASP cc_start: 0.8146 (t0) cc_final: 0.7630 (t0)
REVERT: A  546 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8166 (t0)
REVERT: A  567 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8472 (p0)
REVERT: A  645 ARG cc_start: 0.9133 (ptm-80) cc_final: 0.8783 (tpp80)
REVERT: A  719 ARG cc_start: 0.8042 (mmm160) cc_final: 0.7558 (mmm160)
REVERT: A  987 LYS cc_start: 0.8845 (mtpt) cc_final: 0.8301 (mttm)
REVERT: A  994 CYS cc_start: 0.7955 (m) cc_final: 0.7623 (m)
REVERT: B   11 LYS cc_start: 0.8372 (ptmt) cc_final: 0.8153 (ptmt)
REVERT: B   60 ASN cc_start: 0.8444 (t0) cc_final: 0.7920 (t0)
REVERT: B   64 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8740 (mm-30)
REVERT: C   59 ASP cc_start: 0.8538 (t0) cc_final: 0.8137 (t70)
REVERT: C  116 ASP cc_start: 0.7661 (m-30) cc_final: 0.6909 (t0)
REVERT: C  143 ARG cc_start: 0.8766 (ttp80) cc_final: 0.8246 (ttp-110)
REVERT: D   31 GLN cc_start: 0.8462 (tt0) cc_final: 0.8162 (tp40)
REVERT: D   59 TYR cc_start: 0.8383 (m-80) cc_final: 0.8000 (m-80)
  outliers start: 28
  outliers final: 21
  residues processed: 134
  average time/residue: 0.0904
  time to fit residues: 16.7814
Evaluate side-chains
  135 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  498 MET
Chi-restraints excluded: chain A residue  546 ASP
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  567 ASN
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  588 LYS
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  926 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain D residue   22 THR
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain D residue   70 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 120 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0980
   chunk 96 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0070
   chunk 94 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.5198

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.115125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.081756 restraints weight = 17480.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 3.37
r_work: 0.2976 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10347  Z= 0.100
  Angle     :  0.477   8.121  14011  Z= 0.243
  Chirality :  0.041   0.178   1568
  Planarity :  0.004   0.039   1812
  Dihedral  :  6.326  84.542   1414
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  :  9.65 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.55 (0.24), residues: 1273
  helix:  1.86 (0.23), residues: 516
  sheet:  1.16 (0.35), residues: 205
  loop :  0.27 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 841 
 TYR   0.049   0.001   TYR C  60 
 PHE   0.021   0.001   PHE C  62 
 TRP   0.008   0.001   TRP C  93 
 HIS   0.002   0.000   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (10344)
  covalent geometry    : angle       0.47527 (14009)
  SS BOND              : bond        0.00701 (    1)
  SS BOND              : angle       3.17695 (    2)
  hydrogen bonds       : bond        0.03103 (  477)
  hydrogen bonds       : angle       4.11693 ( 1323)
  Misc. bond           : bond        0.00064 (    2)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8560 (tp30) cc_final: 0.8137 (tp30)
REVERT: A  184 MET cc_start: 0.8318 (mtm) cc_final: 0.7975 (mtt)
REVERT: A  185 ILE cc_start: 0.8576 (mt) cc_final: 0.8271 (mp)
REVERT: A  334 PHE cc_start: 0.7501 (m-80) cc_final: 0.7174 (m-10)
REVERT: A  442 MET cc_start: 0.7521 (tpp) cc_final: 0.6941 (mmm)
REVERT: A  465 ASP cc_start: 0.8132 (t0) cc_final: 0.7615 (t0)
REVERT: A  546 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8126 (t0)
REVERT: A  567 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8479 (p0)
REVERT: A  645 ARG cc_start: 0.9123 (ptm-80) cc_final: 0.8785 (tpp80)
REVERT: A  719 ARG cc_start: 0.8040 (mmm160) cc_final: 0.7557 (mmm160)
REVERT: A  987 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8301 (mttm)
REVERT: A  994 CYS cc_start: 0.7930 (m) cc_final: 0.7595 (m)
REVERT: B   11 LYS cc_start: 0.8366 (ptmt) cc_final: 0.8147 (ptmt)
REVERT: B   60 ASN cc_start: 0.8447 (t0) cc_final: 0.7933 (t0)
REVERT: B   64 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8704 (mm-30)
REVERT: C   59 ASP cc_start: 0.8525 (t0) cc_final: 0.7690 (t70)
REVERT: C  116 ASP cc_start: 0.7643 (m-30) cc_final: 0.6896 (t0)
REVERT: C  130 ASP cc_start: 0.7179 (t0) cc_final: 0.6771 (p0)
REVERT: C  143 ARG cc_start: 0.8767 (ttp80) cc_final: 0.8242 (ttp-110)
REVERT: D   31 GLN cc_start: 0.8456 (tt0) cc_final: 0.8079 (tp40)
REVERT: D   41 GLN cc_start: 0.6972 (mt0) cc_final: 0.6183 (mp10)
REVERT: D   59 TYR cc_start: 0.8398 (m-80) cc_final: 0.8010 (m-80)
  outliers start: 25
  outliers final: 22
  residues processed: 133
  average time/residue: 0.0954
  time to fit residues: 17.6054
Evaluate side-chains
  140 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  498 MET
Chi-restraints excluded: chain A residue  546 ASP
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  567 ASN
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  588 LYS
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  926 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain D residue   22 THR
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain D residue   70 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 79 optimal weight:    0.5980
   chunk 92 optimal weight:    2.9990
   chunk 108 optimal weight:    6.9990
   chunk 81 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.114789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.081502 restraints weight = 17213.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 3.32
r_work: 0.2975 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10347  Z= 0.117
  Angle     :  0.481   8.484  14011  Z= 0.246
  Chirality :  0.041   0.158   1568
  Planarity :  0.004   0.039   1812
  Dihedral  :  6.319  83.883   1414
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  9.91 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.24), residues: 1273
  helix:  1.86 (0.23), residues: 516
  sheet:  1.14 (0.35), residues: 205
  loop :  0.26 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 841 
 TYR   0.014   0.001   TYR C 127 
 PHE   0.013   0.001   PHE C  62 
 TRP   0.008   0.001   TRP C  93 
 HIS   0.002   0.000   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10344)
  covalent geometry    : angle       0.47940 (14009)
  SS BOND              : bond        0.00625 (    1)
  SS BOND              : angle       3.26457 (    2)
  hydrogen bonds       : bond        0.03166 (  477)
  hydrogen bonds       : angle       4.09596 ( 1323)
  Misc. bond           : bond        0.00101 (    2)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8558 (tp30) cc_final: 0.8135 (tp30)
REVERT: A  184 MET cc_start: 0.8302 (mtm) cc_final: 0.8017 (mtt)
REVERT: A  442 MET cc_start: 0.7521 (tpp) cc_final: 0.6937 (mmm)
REVERT: A  465 ASP cc_start: 0.8130 (t0) cc_final: 0.7614 (t0)
REVERT: A  546 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8125 (t0)
REVERT: A  567 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8474 (p0)
REVERT: A  645 ARG cc_start: 0.9132 (ptm-80) cc_final: 0.8783 (tpp80)
REVERT: A  719 ARG cc_start: 0.8038 (mmm160) cc_final: 0.7544 (mmm160)
REVERT: A  987 LYS cc_start: 0.8841 (mtpt) cc_final: 0.8292 (mttm)
REVERT: A  994 CYS cc_start: 0.7903 (m) cc_final: 0.7539 (m)
REVERT: B   11 LYS cc_start: 0.8365 (ptmt) cc_final: 0.8152 (ptmt)
REVERT: B   60 ASN cc_start: 0.8456 (t0) cc_final: 0.7954 (t0)
REVERT: B   64 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8678 (mm-30)
REVERT: C   59 ASP cc_start: 0.8484 (t0) cc_final: 0.7648 (t70)
REVERT: C  130 ASP cc_start: 0.7185 (t0) cc_final: 0.6770 (p0)
REVERT: C  143 ARG cc_start: 0.8767 (ttp80) cc_final: 0.8241 (ttp-110)
REVERT: D   31 GLN cc_start: 0.8456 (tt0) cc_final: 0.8075 (tp40)
REVERT: D   41 GLN cc_start: 0.7075 (mt0) cc_final: 0.6330 (mp10)
REVERT: D   59 TYR cc_start: 0.8418 (m-80) cc_final: 0.8042 (m-80)
  outliers start: 24
  outliers final: 22
  residues processed: 133
  average time/residue: 0.0925
  time to fit residues: 17.4969
Evaluate side-chains
  139 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  498 MET
Chi-restraints excluded: chain A residue  546 ASP
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  567 ASN
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  588 LYS
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  926 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain D residue   22 THR
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain D residue   70 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 105 optimal weight:    2.9990
   chunk 75 optimal weight:    0.2980
   chunk 21 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 94 optimal weight:    0.2980
   chunk 114 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.9982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.113518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.080218 restraints weight = 17439.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 3.34
r_work: 0.2953 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10347  Z= 0.147
  Angle     :  0.503   8.400  14011  Z= 0.255
  Chirality :  0.042   0.143   1568
  Planarity :  0.004   0.055   1812
  Dihedral  :  6.412  84.217   1414
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 10.09 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.24), residues: 1273
  helix:  1.94 (0.24), residues: 508
  sheet:  1.05 (0.37), residues: 192
  loop :  0.18 (0.26), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 841 
 TYR   0.026   0.001   TYR C  60 
 PHE   0.014   0.001   PHE C  62 
 TRP   0.009   0.001   TRP C  93 
 HIS   0.002   0.001   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (10344)
  covalent geometry    : angle       0.50148 (14009)
  SS BOND              : bond        0.00848 (    1)
  SS BOND              : angle       3.28988 (    2)
  hydrogen bonds       : bond        0.03381 (  477)
  hydrogen bonds       : angle       4.16030 ( 1323)
  Misc. bond           : bond        0.00048 (    2)
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 2227.16 seconds
wall clock time: 38 minutes 45.91 seconds (2325.91 seconds total)