Starting phenix.real_space_refine
on Wed Aug  5 12:33:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wf8_37486/08_2026/8wf8_37486.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wf8_37486/08_2026/8wf8_37486.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wf8_37486/08_2026/8wf8_37486.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wf8_37486/08_2026/8wf8_37486.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wf8_37486/08_2026/8wf8_37486.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wf8_37486/08_2026/8wf8_37486.cif"
  }
  resolution = 2.59
  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=   0.002 sd=   0.113
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      55      5.49       5
     Mg      1      5.21       5
     S      44      5.16       5
     C    6107      2.51       5
     N    1723      2.21       5
     O    2025      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9955
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 8785
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1066, 8763
          Classifications: {'peptide': 1066}
          Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 1033}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 1066, 8763
          Classifications: {'peptide': 1066}
          Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 1033}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 8901
    Chain: "B"
      Number of atoms: 1169
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 1169
          Classifications: {'RNA': 55}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 10, 'rna3p_pur': 23, 'rna3p_pyr': 18}
          Link IDs: {'rna2p': 14, 'rna3p': 40}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AARG A  78 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A  78 " occ=0.50
    residue:
      pdb=" N  APHE A1003 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A1003 " occ=0.50
  Time building chain proxies: 4.27, per 1000 atoms: 0.43
  Number of scatterers: 9955
  At special positions: 0
  Unit cell: (87.15, 91.3, 126.16, 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      44     16.00
     P      55     15.00
     Mg      1     11.99
     O    2025      8.00
     N    1723      7.00
     C    6107      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 692.7 milliseconds
  

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2038

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 7 sheets defined
      63.3% alpha, 8.9% beta
      15 base pairs and 25 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 10
    Processing helix  chain 'A' and resid 10 through 37
    Processing helix  chain 'A' and resid 48 through 51
    Processing helix  chain 'A' and resid 52 through 61
      removed outlier: 3.512A  pdb=" N   LEU A  58 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 83
    Processing helix  chain 'A' and resid 84 through 102
      removed outlier: 4.474A  pdb=" N   ILE A  88 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 132
    Processing helix  chain 'A' and resid 138 through 142
    Processing helix  chain 'A' and resid 145 through 151
    Processing helix  chain 'A' and resid 151 through 175
      removed outlier: 3.610A  pdb=" N   VAL A 165 " --> pdb=" O   ASN A 161 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ASN A 171 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLU A 172 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 186
      removed outlier: 4.856A  pdb=" N   PHE A 183 " --> pdb=" O   GLU A 179 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   ILE A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 236
      removed outlier: 4.002A  pdb=" N   PHE A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 247
    Processing helix  chain 'A' and resid 259 through 269
    Processing helix  chain 'A' and resid 286 through 299
    Processing helix  chain 'A' and resid 302 through 307
    Processing helix  chain 'A' and resid 310 through 316
    Processing helix  chain 'A' and resid 335 through 348
    Processing helix  chain 'A' and resid 391 through 400
      removed outlier: 3.803A  pdb=" N   LYS A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 429
    Processing helix  chain 'A' and resid 482 through 494
    Processing helix  chain 'A' and resid 494 through 518
    Processing helix  chain 'A' and resid 525 through 530
    Processing helix  chain 'A' and resid 532 through 536
    Processing helix  chain 'A' and resid 537 through 546
    Processing helix  chain 'A' and resid 552 through 583
    Processing helix  chain 'A' and resid 598 through 613
    Processing helix  chain 'A' and resid 617 through 621
    Processing helix  chain 'A' and resid 625 through 638
    Processing helix  chain 'A' and resid 644 through 658
      removed outlier: 4.060A  pdb=" N   PHE A 655 " --> pdb=" O   PHE A 651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 676
      removed outlier: 3.826A  pdb=" N   VAL A 675 " --> pdb=" O   PHE A 671 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   PHE A 676 " --> pdb=" O   LEU A 672 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 671 through 676'
    Processing helix  chain 'A' and resid 683 through 708
    Processing helix  chain 'A' and resid 721 through 725
    Processing helix  chain 'A' and resid 728 through 739
    Processing helix  chain 'A' and resid 749 through 759
    Processing helix  chain 'A' and resid 760 through 764
    Processing helix  chain 'A' and resid 767 through 771
      removed outlier: 4.088A  pdb=" N   ALA A 771 " --> pdb=" O   PHE A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 784
      removed outlier: 3.533A  pdb=" N   ALA A 778 " --> pdb=" O   THR A 774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 790 through 794
    Processing helix  chain 'A' and resid 799 through 807
    Processing helix  chain 'A' and resid 821 through 831
    Processing helix  chain 'A' and resid 831 through 850
    Processing helix  chain 'A' and resid 858 through 903
      removed outlier: 3.717A  pdb=" N   VAL A 888 " --> pdb=" O   ARG A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 913 through 917
    Processing helix  chain 'A' and resid 924 through 927
    Processing helix  chain 'A' and resid 953 through 955
      No H-bonds generated for 'chain 'A' and resid 953 through 955'
    Processing helix  chain 'A' and resid 956 through 963
    Processing helix  chain 'A' and resid 966 through 975
    Processing helix  chain 'A' and resid 981 through 1013
      Proline residue:  A 996  - end of helix
    Processing helix  chain 'A' and resid 1013 through 1022
      removed outlier: 4.126A  pdb=" N   SER A1017 " --> pdb=" O   TYR A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1027 through 1038
    Processing helix  chain 'A' and resid 1042 through 1058
    Processing helix  chain 'A' and resid 1074 through 1087
    Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 190
    Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 213
    Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 283
      removed outlier: 5.836A  pdb=" N   MET A 930 " --> pdb=" O   GLY A 949 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   GLY A 949 " --> pdb=" O   MET A 930 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 318 through 320
    Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 389
      removed outlier: 6.722A  pdb=" N   ARG A 378 " --> pdb=" O   LYS A 367 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   LYS A 367 " --> pdb=" O   ARG A 378 " (cutoff:3.500A)
      removed outlier: 7.287A  pdb=" N   ARG A 380 " --> pdb=" O   LEU A 365 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   LEU A 365 " --> pdb=" O   ARG A 380 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ILE A 382 " --> pdb=" O   ARG A 363 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   ARG A 363 " --> pdb=" O   ILE A 382 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   GLN A 384 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   LYS A 361 " --> pdb=" O   GLN A 384 " (cutoff:3.500A)
      removed outlier: 5.660A  pdb=" N   LEU A 386 " --> pdb=" O   MET A 359 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 413 through 414
      removed outlier: 4.062A  pdb=" N   LYS A 361 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   GLU A 447 " --> pdb=" O   HIS A 356 " (cutoff:3.500A)
      removed outlier: 11.467A  pdb=" N   ASN A 358 " --> pdb=" O   LYS A 445 " (cutoff:3.500A)
      removed outlier: 16.074A  pdb=" N   LYS A 445 " --> pdb=" O   ASN A 358 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 462 through 464
      removed outlier: 3.751A  pdb=" N   VAL A 462 " --> pdb=" O   VAL A 470 " (cutoff:3.500A)

    499 hydrogen bonds defined for protein.
    1409 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      38 hydrogen bonds
      64 hydrogen bond angles
      0 basepair planarities
      15 basepair parallelities
      25 stacking parallelities
  Total time for adding SS restraints: 2.17

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2051
        1.33 -     1.45: 2938
        1.45 -     1.57: 5077
        1.57 -     1.69: 107
        1.69 -     1.82: 81
  Bond restraints: 10254
  Sorted by residual:
  bond pdb=" CA  ALA A 485 "
       pdb=" CB  ALA A 485 "
    ideal  model  delta    sigma   weight residual
    1.528  1.459  0.069 1.66e-02 3.63e+03 1.73e+01
  bond pdb=" NE  ARG A 885 "
       pdb=" CZ  ARG A 885 "
    ideal  model  delta    sigma   weight residual
    1.326  1.287  0.039 1.10e-02 8.26e+03 1.25e+01
  bond pdb=" CA  SER A 933 "
       pdb=" CB  SER A 933 "
    ideal  model  delta    sigma   weight residual
    1.531  1.474  0.057 1.83e-02 2.99e+03 9.80e+00
  bond pdb=" CA  ALA A 778 "
       pdb=" CB  ALA A 778 "
    ideal  model  delta    sigma   weight residual
    1.528  1.480  0.049 1.56e-02 4.11e+03 9.70e+00
  bond pdb=" O5'   A B  29 "
       pdb=" C5'   A B  29 "
    ideal  model  delta    sigma   weight residual
    1.424  1.472 -0.048 1.60e-02 3.91e+03 8.88e+00
  ... (remaining 10249 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.88: 12802
        2.88 -     5.76: 1110
        5.76 -     8.63: 116
        8.63 -    11.51: 10
       11.51 -    14.39: 3
  Bond angle restraints: 14041
  Sorted by residual:
  angle pdb=" O5'   U B  31 "
        pdb=" C5'   U B  31 "
        pdb=" C4'   U B  31 "
      ideal   model   delta    sigma   weight residual
     109.40  102.93    6.47 8.00e-01 1.56e+00 6.54e+01
  angle pdb=" C4'   C B  -4 "
        pdb=" O4'   C B  -4 "
        pdb=" C1'   C B  -4 "
      ideal   model   delta    sigma   weight residual
     109.70  104.39    5.31 7.00e-01 2.04e+00 5.76e+01
  angle pdb=" O3'   U B  30 "
        pdb=" P     U B  31 "
        pdb=" O5'   U B  31 "
      ideal   model   delta    sigma   weight residual
     104.00   89.61   14.39 1.90e+00 2.77e-01 5.74e+01
  angle pdb=" N   GLU A 743 "
        pdb=" CA  GLU A 743 "
        pdb=" CB  GLU A 743 "
      ideal   model   delta    sigma   weight residual
     110.21  121.44  -11.23 1.59e+00 3.96e-01 4.99e+01
  angle pdb=" CB  GLU A 743 "
        pdb=" CG  GLU A 743 "
        pdb=" CD  GLU A 743 "
      ideal   model   delta    sigma   weight residual
     112.60  124.34  -11.74 1.70e+00 3.46e-01 4.77e+01
  ... (remaining 14036 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.11: 5912
       24.11 -    48.21: 315
       48.21 -    72.32: 120
       72.32 -    96.43: 17
       96.43 -   120.53: 1
  Dihedral angle restraints: 6365
    sinusoidal: 3212
      harmonic: 3153
  Sorted by residual:
  dihedral pdb=" O4'   G B -14 "
           pdb=" C2'   G B -14 "
           pdb=" C1'   G B -14 "
           pdb=" C3'   G B -14 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00  -20.20   45.20     1      8.00e+00 1.56e-02 4.43e+01
  dihedral pdb=" C5'   G B  21 "
           pdb=" C4'   G B  21 "
           pdb=" C3'   G B  21 "
           pdb=" O3'   G B  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  102.37   44.63     1      8.00e+00 1.56e-02 4.32e+01
  dihedral pdb=" O4'   G B  21 "
           pdb=" C4'   G B  21 "
           pdb=" C3'   G B  21 "
           pdb=" C2'   G B  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -17.13   41.13     1      8.00e+00 1.56e-02 3.70e+01
  ... (remaining 6362 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.132: 1360
       0.132 -    0.264: 189
       0.264 -    0.395: 7
       0.395 -    0.527: 0
       0.527 -    0.659: 3
  Chirality restraints: 1559
  Sorted by residual:
  chirality pdb=" P     A B -24 "
            pdb=" OP1   A B -24 "
            pdb=" OP2   A B -24 "
            pdb=" O5'   A B -24 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -3.07   -0.66 2.00e-01 2.50e+01 1.09e+01
  chirality pdb=" P     G B -14 "
            pdb=" OP1   G B -14 "
            pdb=" OP2   G B -14 "
            pdb=" O5'   G B -14 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -3.01   -0.60 2.00e-01 2.50e+01 8.96e+00
  chirality pdb=" P     C B  -9 "
            pdb=" OP1   C B  -9 "
            pdb=" OP2   C B  -9 "
            pdb=" O5'   C B  -9 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    3.01   -0.60 2.00e-01 2.50e+01 8.89e+00
  ... (remaining 1556 not shown)

  Planarity restraints: 1613
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  21 "    0.088 2.00e-02 2.50e+03   3.88e-02 4.51e+01
        pdb=" N9    G B  21 "   -0.059 2.00e-02 2.50e+03
        pdb=" C8    G B  21 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    G B  21 "   -0.028 2.00e-02 2.50e+03
        pdb=" C5    G B  21 "   -0.021 2.00e-02 2.50e+03
        pdb=" C6    G B  21 "    0.050 2.00e-02 2.50e+03
        pdb=" O6    G B  21 "    0.026 2.00e-02 2.50e+03
        pdb=" N1    G B  21 "    0.010 2.00e-02 2.50e+03
        pdb=" C2    G B  21 "   -0.029 2.00e-02 2.50e+03
        pdb=" N2    G B  21 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3    G B  21 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G B  21 "   -0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  29 "   -0.063 2.00e-02 2.50e+03   3.18e-02 2.78e+01
        pdb=" N9    A B  29 "    0.073 2.00e-02 2.50e+03
        pdb=" C8    A B  29 "   -0.016 2.00e-02 2.50e+03
        pdb=" N7    A B  29 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5    A B  29 "    0.025 2.00e-02 2.50e+03
        pdb=" C6    A B  29 "   -0.008 2.00e-02 2.50e+03
        pdb=" N6    A B  29 "   -0.014 2.00e-02 2.50e+03
        pdb=" N1    A B  29 "   -0.021 2.00e-02 2.50e+03
        pdb=" C2    A B  29 "    0.005 2.00e-02 2.50e+03
        pdb=" N3    A B  29 "    0.009 2.00e-02 2.50e+03
        pdb=" C4    A B  29 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 162 "   -0.068 2.00e-02 2.50e+03   3.49e-02 2.44e+01
        pdb=" CG  TYR A 162 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 162 "    0.035 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 162 "    0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 162 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 162 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 162 "   -0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR A 162 "   -0.039 2.00e-02 2.50e+03
  ... (remaining 1610 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 115
        2.64 -     3.20: 8714
        3.20 -     3.77: 16384
        3.77 -     4.33: 23339
        4.33 -     4.90: 35136
  Nonbonded interactions: 83688
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 345 "
            pdb=" OH  TYR A 439 "
     model   vdw
     2.070 3.040
  nonbonded pdb=" OP1   G B  23 "
            pdb="MG    MG A1101 "
     model   vdw
     2.144 2.170
  nonbonded pdb=" OE1 GLN A 747 "
            pdb="MG    MG A1101 "
     model   vdw
     2.210 2.170
  nonbonded pdb=" ND1 HIS A 282 "
            pdb=" O4    U B  -5 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" O   PHE A 406 "
            pdb=" OG  SER A 409 "
     model   vdw
     2.345 3.040
  ... (remaining 83683 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.50 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:             1.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.190
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8904
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   0.069  10254  Z= 0.615
  Angle     :  1.709  14.390  14041  Z= 1.121
  Chirality :  0.091   0.659   1559
  Planarity :  0.009   0.092   1613
  Dihedral  : 16.809 120.534   4327
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 0.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  4.05 %
    Favored  : 94.81 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.23), residues: 1064
  helix: -1.34 (0.17), residues: 597
  sheet:  0.09 (0.74), residues: 50
  loop :  0.22 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.045   0.005   ARG A 412 
 TYR   0.068   0.009   TYR A 162 
 PHE   0.047   0.009   PHE A 819 
 TRP   0.037   0.010   TRP A 724 
 HIS   0.010   0.004   HIS A 223 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00958 /  0.61 (10254)
  covalent geometry    : angle       1.70926 /  1.12 (14041)
  hydrogen bonds       : bond        0.18374 / 12.44 (  537)
  hydrogen bonds       : angle       6.81719 /  4.83 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 176
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8235 (mttt) cc_final: 0.7538 (mttp)
REVERT: A   95 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8053 (mt-10)
REVERT: A  158 MET cc_start: 0.8311 (mtp) cc_final: 0.8004 (mtp)
REVERT: A  172 GLU cc_start: 0.8049 (tt0) cc_final: 0.7545 (mt-10)
REVERT: A  187 LYS cc_start: 0.8540 (mttt) cc_final: 0.8284 (mmtm)
REVERT: A  190 LYS cc_start: 0.7645 (tttt) cc_final: 0.6804 (ptmt)
REVERT: A  202 GLN cc_start: 0.7604 (mt0) cc_final: 0.6758 (mm110)
REVERT: A  220 LYS cc_start: 0.8142 (mttt) cc_final: 0.7440 (mmpt)
REVERT: A  221 LYS cc_start: 0.7947 (mttt) cc_final: 0.7562 (mmtm)
REVERT: A  239 LYS cc_start: 0.8568 (mttt) cc_final: 0.7735 (mmtm)
REVERT: A  248 ARG cc_start: 0.8189 (mmt180) cc_final: 0.7939 (mmt180)
REVERT: A  323 ASP cc_start: 0.6792 (p0) cc_final: 0.6528 (t0)
REVERT: A  380 ARG cc_start: 0.8400 (tpt170) cc_final: 0.8171 (tpt170)
REVERT: A  393 GLU cc_start: 0.8353 (tt0) cc_final: 0.7715 (tp30)
REVERT: A  412 ARG cc_start: 0.8645 (ptt-90) cc_final: 0.7641 (ptt90)
REVERT: A  415 ASP cc_start: 0.8066 (m-30) cc_final: 0.7621 (t70)
REVERT: A  417 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6934 (mm-30)
REVERT: A  419 MET cc_start: 0.7134 (mtm) cc_final: 0.6819 (ttm)
REVERT: A  420 LYS cc_start: 0.7434 (mttt) cc_final: 0.6972 (mptp)
REVERT: A  497 LYS cc_start: 0.8689 (mttt) cc_final: 0.8460 (mmmm)
REVERT: A  514 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8041 (mm-40)
REVERT: A  558 ARG cc_start: 0.7899 (ttt-90) cc_final: 0.7044 (ttp-110)
REVERT: A  570 ARG cc_start: 0.7688 (ttt180) cc_final: 0.7309 (ttm110)
REVERT: A  574 ARG cc_start: 0.8369 (ttt180) cc_final: 0.7468 (ttm110)
REVERT: A  579 ARG cc_start: 0.8290 (mtp180) cc_final: 0.8046 (mtp180)
REVERT: A  580 LYS cc_start: 0.7945 (tttt) cc_final: 0.6954 (ttpp)
REVERT: A  601 LYS cc_start: 0.8524 (tptt) cc_final: 0.8108 (ttmt)
REVERT: A  657 LYS cc_start: 0.8466 (mmtp) cc_final: 0.7547 (mtmt)
REVERT: A  705 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7323 (mm-30)
REVERT: A  725 LYS cc_start: 0.8370 (mttt) cc_final: 0.7692 (mptp)
REVERT: A  786 ASP cc_start: 0.8107 (m-30) cc_final: 0.7843 (t70)
REVERT: A  794 GLN cc_start: 0.8725 (mt0) cc_final: 0.8426 (mp10)
REVERT: A  800 ARG cc_start: 0.8363 (ttp-110) cc_final: 0.7587 (tpm170)
REVERT: A  816 GLN cc_start: 0.8283 (mt0) cc_final: 0.7751 (mm-40)
REVERT: A  817 HIS cc_start: 0.8786 (m170) cc_final: 0.8522 (m90)
REVERT: A  837 GLU cc_start: 0.7643 (tt0) cc_final: 0.6925 (mt-10)
REVERT: A  864 ILE cc_start: 0.7461 (mt) cc_final: 0.7149 (mp)
REVERT: A  867 LYS cc_start: 0.8261 (mttt) cc_final: 0.7307 (tttt)
REVERT: A  941 LYS cc_start: 0.8723 (mttt) cc_final: 0.8101 (mtmt)
REVERT: A  972 GLU cc_start: 0.8258 (tp30) cc_final: 0.7767 (tt0)
REVERT: A  985 MET cc_start: 0.8791 (mtp) cc_final: 0.8558 (mtt)
REVERT: A 1029 LYS cc_start: 0.7608 (tttt) cc_final: 0.6801 (mptt)
REVERT: A 1044 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6448 (tt0)
REVERT: A 1068 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7541 (mp0)
REVERT: A 1070 LYS cc_start: 0.8141 (mttt) cc_final: 0.7479 (mtmt)
  outliers start: 11
  outliers final: 4
  residues processed: 185
  average time/residue: 0.8416
  time to fit residues: 163.8078
Evaluate side-chains
  158 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 154
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  834 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    9.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  57 HIS
A  92 ASN
A 103 GLN
A 153 GLN
A 171 ASN
A 219 GLN
A 240 GLN
A 256 ASN
A 287 ASN
A 710 ASN
A 816 GLN
A 842 GLN
A 993 GLN
A1004 ASN
A1054 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.135820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.105951 restraints weight = 20882.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 2.26
r_work: 0.2896 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2780
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2780 r_free = 0.2780    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2780 r_free = 0.2780    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (6 function evaluations)
r_final: 0.2780
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8971
moved from start:          0.1362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10254  Z= 0.157
  Angle     :  0.604   6.616  14041  Z= 0.339
  Chirality :  0.043   0.194   1559
  Planarity :  0.004   0.033   1613
  Dihedral  : 16.226 115.937   2045
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  5.91 %
    Favored  : 92.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.25), residues: 1064
  helix:  1.42 (0.20), residues: 603
  sheet: -0.21 (0.70), residues: 49
  loop :  0.67 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 579 
 TYR   0.022   0.002   TYR A 886 
 PHE   0.019   0.002   PHE A 792 
 TRP   0.010   0.001   TRP A 724 
 HIS   0.005   0.001   HIS A 669 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.16 (10254)
  covalent geometry    : angle       0.60410 /  0.34 (14041)
  hydrogen bonds       : bond        0.06850 /  4.60 (  537)
  hydrogen bonds       : angle       4.43604 /  3.15 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 165
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8383 (mttt) cc_final: 0.7820 (mttp)
REVERT: A   95 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7770 (mt-10)
REVERT: A  158 MET cc_start: 0.8242 (mtp) cc_final: 0.7993 (mtp)
REVERT: A  172 GLU cc_start: 0.8144 (tt0) cc_final: 0.7750 (mt-10)
REVERT: A  190 LYS cc_start: 0.7889 (tttt) cc_final: 0.7301 (ptpt)
REVERT: A  202 GLN cc_start: 0.7764 (mt0) cc_final: 0.7187 (mm110)
REVERT: A  220 LYS cc_start: 0.8643 (mttt) cc_final: 0.8246 (mmpt)
REVERT: A  239 LYS cc_start: 0.8320 (mttt) cc_final: 0.7726 (mmtm)
REVERT: A  380 ARG cc_start: 0.8297 (tpt170) cc_final: 0.8004 (tpt170)
REVERT: A  393 GLU cc_start: 0.8192 (tt0) cc_final: 0.7888 (tp30)
REVERT: A  412 ARG cc_start: 0.8557 (ptt-90) cc_final: 0.7890 (ptt90)
REVERT: A  419 MET cc_start: 0.7784 (mtm) cc_final: 0.7417 (ttm)
REVERT: A  514 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8028 (mm-40)
REVERT: A  533 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7852 (tp30)
REVERT: A  558 ARG cc_start: 0.7922 (ttt-90) cc_final: 0.7348 (ttp-110)
REVERT: A  574 ARG cc_start: 0.8343 (ttt180) cc_final: 0.7778 (ttm110)
REVERT: A  579 ARG cc_start: 0.8045 (mtp180) cc_final: 0.7832 (mtp180)
REVERT: A  580 LYS cc_start: 0.8142 (tttt) cc_final: 0.7530 (ttpp)
REVERT: A  589 MET cc_start: 0.8928 (ttt) cc_final: 0.8475 (ttt)
REVERT: A  657 LYS cc_start: 0.8625 (mmtp) cc_final: 0.7828 (mtmt)
REVERT: A  705 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7820 (mm-30)
REVERT: A  725 LYS cc_start: 0.8398 (mttt) cc_final: 0.7945 (mptp)
REVERT: A  794 GLN cc_start: 0.8435 (mt0) cc_final: 0.8112 (mp10)
REVERT: A  800 ARG cc_start: 0.8200 (ttp-110) cc_final: 0.7883 (tpm170)
REVERT: A  816 GLN cc_start: 0.8495 (mt0) cc_final: 0.8041 (mm-40)
REVERT: A  817 HIS cc_start: 0.8904 (m170) cc_final: 0.8590 (m-70)
REVERT: A  837 GLU cc_start: 0.8040 (tt0) cc_final: 0.7513 (mt-10)
REVERT: A  864 ILE cc_start: 0.7718 (mt) cc_final: 0.7502 (mm)
REVERT: A  867 LYS cc_start: 0.8434 (mttt) cc_final: 0.7834 (tttt)
REVERT: A 1029 LYS cc_start: 0.7820 (tttt) cc_final: 0.7242 (mppt)
REVERT: A 1068 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7679 (mp0)
REVERT: A 1070 LYS cc_start: 0.8380 (mttt) cc_final: 0.8021 (mtmt)
REVERT: A 1085 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8178 (mt-10)
  outliers start: 12
  outliers final: 5
  residues processed: 175
  average time/residue: 0.8655
  time to fit residues: 159.0583
Evaluate side-chains
  157 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 150
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue 1085 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0980
   chunk 61 optimal weight:    2.9990
   chunk 104 optimal weight:    3.9990
   chunk 69 optimal weight:    0.1980
   chunk 106 optimal weight:   20.0000
   chunk 60 optimal weight:    3.9990
   chunk 96 optimal weight:    3.9990
   chunk 74 optimal weight:    0.2980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  60 ASN
A  63 ASN
A  92 ASN
A 103 GLN
A 219 GLN
A 240 GLN
A 325 ASN
A 596 GLN
A 710 ASN
A 747 GLN
A 842 GLN
A1004 ASN
A1045 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.138170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.108467 restraints weight = 23261.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.42
r_work: 0.2907 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (14 function evaluations)
r_final: 0.2791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8958
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10254  Z= 0.130
  Angle     :  0.509   5.988  14041  Z= 0.283
  Chirality :  0.040   0.152   1559
  Planarity :  0.004   0.032   1613
  Dihedral  : 16.137 111.859   2045
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  7.57 %
    Favored  : 91.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.21 (0.25), residues: 1064
  helix:  2.18 (0.20), residues: 608
  sheet:  0.29 (0.75), residues: 42
  loop :  0.62 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 695 
 TYR   0.020   0.002   TYR A 886 
 PHE   0.016   0.002   PHE A 958 
 TRP   0.005   0.001   TRP A 724 
 HIS   0.005   0.001   HIS A 669 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.13 (10254)
  covalent geometry    : angle       0.50899 /  0.28 (14041)
  hydrogen bonds       : bond        0.05627 /  3.81 (  537)
  hydrogen bonds       : angle       4.02336 /  2.83 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 154
  time to evaluate  : 0.418 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8359 (mttt) cc_final: 0.7968 (mtmm)
REVERT: A  172 GLU cc_start: 0.8084 (tt0) cc_final: 0.7651 (mt-10)
REVERT: A  190 LYS cc_start: 0.7883 (tttt) cc_final: 0.7288 (ptpt)
REVERT: A  202 GLN cc_start: 0.7763 (mt0) cc_final: 0.7143 (mm110)
REVERT: A  220 LYS cc_start: 0.8595 (mttt) cc_final: 0.8116 (mmpt)
REVERT: A  239 LYS cc_start: 0.8367 (mttt) cc_final: 0.7710 (mmtm)
REVERT: A  248 ARG cc_start: 0.8624 (mmt180) cc_final: 0.8386 (mmt180)
REVERT: A  393 GLU cc_start: 0.8236 (tt0) cc_final: 0.7903 (tp30)
REVERT: A  412 ARG cc_start: 0.8557 (ptt-90) cc_final: 0.7871 (ptt90)
REVERT: A  419 MET cc_start: 0.7887 (mtm) cc_final: 0.7505 (mtm)
REVERT: A  533 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7946 (tp30)
REVERT: A  558 ARG cc_start: 0.7847 (ttt-90) cc_final: 0.7310 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8395 (tttt) cc_final: 0.7596 (ttpp)
REVERT: A  574 ARG cc_start: 0.8444 (ttt180) cc_final: 0.7817 (ttm110)
REVERT: A  579 ARG cc_start: 0.8016 (mtp180) cc_final: 0.7815 (mtp180)
REVERT: A  580 LYS cc_start: 0.8124 (tttt) cc_final: 0.7854 (tttp)
REVERT: A  657 LYS cc_start: 0.8538 (mmtp) cc_final: 0.7781 (mppt)
REVERT: A  705 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7938 (mm-30)
REVERT: A  725 LYS cc_start: 0.8352 (mttt) cc_final: 0.7867 (mptp)
REVERT: A  794 GLN cc_start: 0.8474 (mt0) cc_final: 0.8162 (mp10)
REVERT: A  800 ARG cc_start: 0.8179 (ttp-110) cc_final: 0.7876 (tpm170)
REVERT: A  816 GLN cc_start: 0.8466 (mt0) cc_final: 0.8032 (mm-40)
REVERT: A  817 HIS cc_start: 0.8860 (m170) cc_final: 0.8591 (m-70)
REVERT: A  837 GLU cc_start: 0.8059 (tt0) cc_final: 0.7579 (tp30)
REVERT: A  841 LYS cc_start: 0.7589 (tttp) cc_final: 0.7049 (mtmt)
REVERT: A  867 LYS cc_start: 0.8421 (mttt) cc_final: 0.7787 (tttt)
REVERT: A  942 LYS cc_start: 0.8572 (tttt) cc_final: 0.8354 (tttp)
REVERT: A 1029 LYS cc_start: 0.7714 (tttt) cc_final: 0.7209 (mppt)
REVERT: A 1068 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7544 (mp0)
REVERT: A 1070 LYS cc_start: 0.8299 (mttt) cc_final: 0.7938 (mtmt)
REVERT: A 1089 MET cc_start: 0.7706 (mmt) cc_final: 0.7337 (mmt)
  outliers start: 11
  outliers final: 5
  residues processed: 160
  average time/residue: 0.8410
  time to fit residues: 141.4378
Evaluate side-chains
  156 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 150
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue 1067 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 109 optimal weight:    9.9990
   chunk 77 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  92 ASN
A 103 GLN
A 219 GLN
A 240 GLN
A 325 ASN
A 596 GLN
A 710 ASN
A 842 GLN
A1004 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.138224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.111145 restraints weight = 13396.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 1.43
r_work: 0.2890 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2716
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (8 function evaluations)
r_final: 0.2716
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8947
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10254  Z= 0.127
  Angle     :  0.487   5.337  14041  Z= 0.270
  Chirality :  0.039   0.145   1559
  Planarity :  0.004   0.035   1613
  Dihedral  : 16.026 109.741   2045
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  7.99 %
    Favored  : 90.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.39 (0.25), residues: 1064
  helix:  2.36 (0.20), residues: 607
  sheet:  0.45 (0.80), residues: 42
  loop :  0.63 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 695 
 TYR   0.021   0.002   TYR A  17 
 PHE   0.015   0.001   PHE A 792 
 TRP   0.005   0.001   TRP A 724 
 HIS   0.004   0.001   HIS A 669 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.13 (10254)
  covalent geometry    : angle       0.48676 /  0.27 (14041)
  hydrogen bonds       : bond        0.05448 /  3.68 (  537)
  hydrogen bonds       : angle       3.94767 /  2.78 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 153
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8312 (mttt) cc_final: 0.7844 (mtmm)
REVERT: A  172 GLU cc_start: 0.8070 (tt0) cc_final: 0.7566 (mt-10)
REVERT: A  190 LYS cc_start: 0.7868 (tttt) cc_final: 0.7202 (ptpt)
REVERT: A  202 GLN cc_start: 0.7769 (mt0) cc_final: 0.6997 (mm110)
REVERT: A  220 LYS cc_start: 0.8586 (mttt) cc_final: 0.8184 (mmtm)
REVERT: A  239 LYS cc_start: 0.8245 (mttt) cc_final: 0.7571 (mmtm)
REVERT: A  393 GLU cc_start: 0.8361 (tt0) cc_final: 0.7890 (tp30)
REVERT: A  412 ARG cc_start: 0.8539 (ptt-90) cc_final: 0.7785 (ptt90)
REVERT: A  533 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7869 (tp30)
REVERT: A  558 ARG cc_start: 0.7871 (ttt-90) cc_final: 0.7191 (ttp-110)
REVERT: A  574 ARG cc_start: 0.8518 (ttt180) cc_final: 0.7748 (ttm110)
REVERT: A  579 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7781 (mtp180)
REVERT: A  589 MET cc_start: 0.8916 (ttt) cc_final: 0.8523 (ttt)
REVERT: A  608 LYS cc_start: 0.8759 (ttpt) cc_final: 0.8457 (ttmt)
REVERT: A  657 LYS cc_start: 0.8574 (mmtp) cc_final: 0.7754 (mppt)
REVERT: A  705 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7859 (mm-30)
REVERT: A  725 LYS cc_start: 0.8332 (mttt) cc_final: 0.7815 (mptp)
REVERT: A  794 GLN cc_start: 0.8629 (mt0) cc_final: 0.8307 (mp10)
REVERT: A  800 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.7854 (tpm170)
REVERT: A  816 GLN cc_start: 0.8482 (mt0) cc_final: 0.8020 (mm-40)
REVERT: A  837 GLU cc_start: 0.8166 (tt0) cc_final: 0.7520 (tp30)
REVERT: A  841 LYS cc_start: 0.7605 (tttp) cc_final: 0.7009 (mtmt)
REVERT: A  867 LYS cc_start: 0.8349 (mttt) cc_final: 0.7588 (tttm)
REVERT: A  908 ASP cc_start: 0.6778 (OUTLIER) cc_final: 0.6159 (t0)
REVERT: A 1029 LYS cc_start: 0.7562 (tttt) cc_final: 0.7095 (mppt)
REVERT: A 1068 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7578 (mp0)
REVERT: A 1070 LYS cc_start: 0.8357 (mttt) cc_final: 0.7899 (mtmt)
REVERT: A 1089 MET cc_start: 0.7664 (mmt) cc_final: 0.7429 (mmt)
  outliers start: 11
  outliers final: 6
  residues processed: 161
  average time/residue: 0.8173
  time to fit residues: 138.0957
Evaluate side-chains
  155 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 147
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue  908 ASP
Chi-restraints excluded: chain A residue  927 SER
Chi-restraints excluded: chain A residue 1067 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 82 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   chunk 68 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  92 ASN
A 103 GLN
A 219 GLN
A 240 GLN
A 325 ASN
A 596 GLN
A 710 ASN
A 842 GLN
A1004 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.139224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.109608 restraints weight = 21779.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 2.31
r_work: 0.2944 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2827
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2827 r_free = 0.2827    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2827 r_free = 0.2827    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2827
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8929
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10254  Z= 0.116
  Angle     :  0.462   5.358  14041  Z= 0.257
  Chirality :  0.038   0.143   1559
  Planarity :  0.004   0.034   1613
  Dihedral  : 15.959 108.654   2044
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  8.51 %
    Favored  : 90.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.49 (0.25), residues: 1064
  helix:  2.48 (0.20), residues: 607
  sheet:  0.43 (0.81), residues: 42
  loop :  0.64 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 695 
 TYR   0.020   0.001   TYR A  17 
 PHE   0.015   0.001   PHE A 792 
 TRP   0.005   0.001   TRP A 724 
 HIS   0.004   0.001   HIS A 669 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.12 (10254)
  covalent geometry    : angle       0.46222 /  0.26 (14041)
  hydrogen bonds       : bond        0.05170 /  3.49 (  537)
  hydrogen bonds       : angle       3.85291 /  2.71 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8287 (mttt) cc_final: 0.7944 (mtmm)
REVERT: A  172 GLU cc_start: 0.8051 (tt0) cc_final: 0.7608 (mt-10)
REVERT: A  190 LYS cc_start: 0.7868 (tttt) cc_final: 0.7326 (ptpt)
REVERT: A  202 GLN cc_start: 0.7638 (mt0) cc_final: 0.7054 (mm110)
REVERT: A  220 LYS cc_start: 0.8605 (mttt) cc_final: 0.8296 (mmtt)
REVERT: A  239 LYS cc_start: 0.8252 (mttt) cc_final: 0.7680 (mmtm)
REVERT: A  393 GLU cc_start: 0.8160 (tt0) cc_final: 0.7864 (tp30)
REVERT: A  412 ARG cc_start: 0.8472 (ptt-90) cc_final: 0.7841 (ptt90)
REVERT: A  453 LYS cc_start: 0.8587 (mttp) cc_final: 0.8138 (mmpt)
REVERT: A  533 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7889 (tp30)
REVERT: A  558 ARG cc_start: 0.7764 (ttt-90) cc_final: 0.7291 (ttp-110)
REVERT: A  574 ARG cc_start: 0.8371 (ttt180) cc_final: 0.7746 (ttm110)
REVERT: A  589 MET cc_start: 0.8814 (ttt) cc_final: 0.8398 (ttt)
REVERT: A  608 LYS cc_start: 0.8678 (ttpt) cc_final: 0.8417 (ttmt)
REVERT: A  705 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7848 (mm-30)
REVERT: A  725 LYS cc_start: 0.8267 (mttt) cc_final: 0.7834 (mptp)
REVERT: A  794 GLN cc_start: 0.8333 (mt0) cc_final: 0.8074 (mp10)
REVERT: A  800 ARG cc_start: 0.8090 (ttp-110) cc_final: 0.7809 (tpm170)
REVERT: A  816 GLN cc_start: 0.8424 (mt0) cc_final: 0.7977 (mm-40)
REVERT: A  837 GLU cc_start: 0.7969 (tt0) cc_final: 0.7509 (tp30)
REVERT: A  841 LYS cc_start: 0.7646 (tttp) cc_final: 0.7148 (mtmt)
REVERT: A  867 LYS cc_start: 0.8340 (mttt) cc_final: 0.7673 (tttm)
REVERT: A  908 ASP cc_start: 0.6716 (OUTLIER) cc_final: 0.6181 (t0)
REVERT: A 1029 LYS cc_start: 0.7598 (tttt) cc_final: 0.7248 (mppt)
REVERT: A 1068 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7529 (mp0)
REVERT: A 1070 LYS cc_start: 0.8291 (mttt) cc_final: 0.7895 (mtmt)
REVERT: A 1085 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8087 (mt-10)
REVERT: A 1089 MET cc_start: 0.7596 (mmt) cc_final: 0.7384 (mmt)
  outliers start: 12
  outliers final: 7
  residues processed: 160
  average time/residue: 0.7800
  time to fit residues: 131.1724
Evaluate side-chains
  159 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 149
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue  908 ASP
Chi-restraints excluded: chain A residue  927 SER
Chi-restraints excluded: chain A residue 1067 VAL
Chi-restraints excluded: chain A residue 1085 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 105 optimal weight:    0.9990
   chunk 107 optimal weight:   10.0000
   chunk 13 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  92 ASN
A 103 GLN
A 219 GLN
A 256 ASN
A 596 GLN
A 710 ASN
A 842 GLN
A1004 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.138304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.108740 restraints weight = 19384.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.11
r_work: 0.2939 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2702
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2702
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8995
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      :  0.003   0.048  10254  Z= 0.132
  Angle     :  0.480   5.362  14041  Z= 0.265
  Chirality :  0.039   0.146   1559
  Planarity :  0.004   0.039   1613
  Dihedral  : 15.968 108.175   2044
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  7.99 %
    Favored  : 90.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.49 (0.25), residues: 1064
  helix:  2.45 (0.20), residues: 607
  sheet:  0.53 (0.81), residues: 42
  loop :  0.67 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 695 
 TYR   0.021   0.002   TYR A  17 
 PHE   0.017   0.001   PHE A 792 
 TRP   0.004   0.001   TRP A  50 
 HIS   0.005   0.001   HIS A 669 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 (10254)
  covalent geometry    : angle       0.48045 /  0.27 (14041)
  hydrogen bonds       : bond        0.05367 /  3.62 (  537)
  hydrogen bonds       : angle       3.86885 /  2.73 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8413 (mttt) cc_final: 0.8076 (mtmm)
REVERT: A  172 GLU cc_start: 0.8172 (tt0) cc_final: 0.7704 (mt-10)
REVERT: A  190 LYS cc_start: 0.7948 (tttt) cc_final: 0.7347 (ptpt)
REVERT: A  202 GLN cc_start: 0.7702 (mt0) cc_final: 0.7094 (mm110)
REVERT: A  220 LYS cc_start: 0.8593 (mttt) cc_final: 0.8254 (mmtt)
REVERT: A  239 LYS cc_start: 0.8366 (mttt) cc_final: 0.7739 (mmtm)
REVERT: A  393 GLU cc_start: 0.8373 (tt0) cc_final: 0.7955 (tp30)
REVERT: A  412 ARG cc_start: 0.8618 (ptt-90) cc_final: 0.7929 (ptt90)
REVERT: A  453 LYS cc_start: 0.8594 (mttp) cc_final: 0.8061 (mmpt)
REVERT: A  533 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7938 (tp30)
REVERT: A  558 ARG cc_start: 0.7929 (ttt-90) cc_final: 0.7340 (ttp-110)
REVERT: A  574 ARG cc_start: 0.8512 (ttt180) cc_final: 0.7835 (ttm110)
REVERT: A  589 MET cc_start: 0.8919 (ttt) cc_final: 0.8502 (ttt)
REVERT: A  705 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7979 (mm-30)
REVERT: A  725 LYS cc_start: 0.8332 (mttt) cc_final: 0.7948 (mptp)
REVERT: A  794 GLN cc_start: 0.8597 (mt0) cc_final: 0.8323 (mp10)
REVERT: A  800 ARG cc_start: 0.8355 (ttp-110) cc_final: 0.7924 (tpm170)
REVERT: A  841 LYS cc_start: 0.7713 (tttp) cc_final: 0.7179 (mtmt)
REVERT: A  867 LYS cc_start: 0.8432 (mttt) cc_final: 0.7715 (tttm)
REVERT: A  908 ASP cc_start: 0.6668 (OUTLIER) cc_final: 0.6093 (t0)
REVERT: A 1029 LYS cc_start: 0.7608 (tttt) cc_final: 0.7222 (mppt)
REVERT: A 1068 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7672 (mp0)
REVERT: A 1070 LYS cc_start: 0.8340 (mttt) cc_final: 0.7936 (mtmt)
REVERT: A 1085 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8264 (mt-10)
  outliers start: 14
  outliers final: 7
  residues processed: 156
  average time/residue: 0.8403
  time to fit residues: 137.8529
Evaluate side-chains
  156 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 146
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue  908 ASP
Chi-restraints excluded: chain A residue  927 SER
Chi-restraints excluded: chain A residue 1067 VAL
Chi-restraints excluded: chain A residue 1085 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 67 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  63 ASN
A  92 ASN
A 103 GLN
A 219 GLN
A 256 ASN
A 596 GLN
A 710 ASN
A 842 GLN
A1004 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.137788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.108557 restraints weight = 20063.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 2.20
r_work: 0.2912 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2809
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2809 r_free = 0.2809    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2809 r_free = 0.2809    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2809
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8956
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10254  Z= 0.143
  Angle     :  0.493   5.354  14041  Z= 0.271
  Chirality :  0.040   0.149   1559
  Planarity :  0.004   0.039   1613
  Dihedral  : 16.001 108.002   2044
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  8.51 %
    Favored  : 90.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.25), residues: 1064
  helix:  2.40 (0.20), residues: 607
  sheet:  0.58 (0.81), residues: 42
  loop :  0.68 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 695 
 TYR   0.022   0.002   TYR A  17 
 PHE   0.018   0.002   PHE A 792 
 TRP   0.003   0.001   TRP A  50 
 HIS   0.005   0.001   HIS A 669 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.14 (10254)
  covalent geometry    : angle       0.49327 /  0.27 (14041)
  hydrogen bonds       : bond        0.05534 /  3.72 (  537)
  hydrogen bonds       : angle       3.89272 /  2.75 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 0.413 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8390 (mttt) cc_final: 0.7912 (mtmm)
REVERT: A  172 GLU cc_start: 0.8070 (tt0) cc_final: 0.7632 (mt-10)
REVERT: A  190 LYS cc_start: 0.7876 (tttt) cc_final: 0.7343 (ptpt)
REVERT: A  202 GLN cc_start: 0.7630 (mt0) cc_final: 0.7043 (mm110)
REVERT: A  220 LYS cc_start: 0.8619 (mttt) cc_final: 0.8325 (mmtt)
REVERT: A  239 LYS cc_start: 0.8280 (mttt) cc_final: 0.7631 (mmtm)
REVERT: A  393 GLU cc_start: 0.8218 (tt0) cc_final: 0.7931 (tp30)
REVERT: A  412 ARG cc_start: 0.8483 (ptt-90) cc_final: 0.7859 (ptt90)
REVERT: A  453 LYS cc_start: 0.8592 (mttp) cc_final: 0.8140 (mmpt)
REVERT: A  533 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7892 (tp30)
REVERT: A  558 ARG cc_start: 0.7763 (ttt-90) cc_final: 0.7274 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8365 (tttt) cc_final: 0.7591 (ttpp)
REVERT: A  574 ARG cc_start: 0.8415 (ttt180) cc_final: 0.7773 (ttm110)
REVERT: A  589 MET cc_start: 0.8831 (ttt) cc_final: 0.8399 (ttt)
REVERT: A  705 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7871 (mm-30)
REVERT: A  725 LYS cc_start: 0.8257 (mttt) cc_final: 0.7999 (mttp)
REVERT: A  794 GLN cc_start: 0.8384 (mt0) cc_final: 0.8119 (mp10)
REVERT: A  800 ARG cc_start: 0.8131 (ttp-110) cc_final: 0.7816 (tpm170)
REVERT: A  841 LYS cc_start: 0.7684 (tttp) cc_final: 0.7159 (mtmt)
REVERT: A  867 LYS cc_start: 0.8335 (mttt) cc_final: 0.7665 (tttm)
REVERT: A  908 ASP cc_start: 0.6744 (OUTLIER) cc_final: 0.6195 (t0)
REVERT: A 1029 LYS cc_start: 0.7593 (tttt) cc_final: 0.7222 (mppt)
REVERT: A 1068 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7579 (mp0)
REVERT: A 1070 LYS cc_start: 0.8288 (mttt) cc_final: 0.7909 (mtmt)
REVERT: A 1085 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8048 (mt-10)
  outliers start: 12
  outliers final: 7
  residues processed: 152
  average time/residue: 0.8212
  time to fit residues: 131.2740
Evaluate side-chains
  153 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 143
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue  908 ASP
Chi-restraints excluded: chain A residue  927 SER
Chi-restraints excluded: chain A residue 1067 VAL
Chi-restraints excluded: chain A residue 1085 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 16 optimal weight:    4.9990
   chunk 83 optimal weight:    9.9990
   chunk 13 optimal weight:    0.6980
   chunk 4 optimal weight:    0.1980
   chunk 92 optimal weight:    1.9990
   chunk 88 optimal weight:    7.9990
   chunk 52 optimal weight:    0.1980
   chunk 91 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.4780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  63 ASN
A  68 GLN
A  92 ASN
A 103 GLN
A 219 GLN
A 596 GLN
A 710 ASN
A 842 GLN
A1004 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.141063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.111537 restraints weight = 21738.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 2.24
r_work: 0.2972 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2871
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2871
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8895
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10254  Z= 0.099
  Angle     :  0.434   5.443  14041  Z= 0.243
  Chirality :  0.036   0.148   1559
  Planarity :  0.003   0.045   1613
  Dihedral  : 15.912 105.911   2044
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.13 %
    Favored  : 89.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.68 (0.25), residues: 1064
  helix:  2.59 (0.20), residues: 608
  sheet:  0.96 (0.83), residues: 44
  loop :  0.73 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 695 
 TYR   0.019   0.001   TYR A  17 
 PHE   0.013   0.001   PHE A 792 
 TRP   0.006   0.001   TRP A 724 
 HIS   0.003   0.001   HIS A 669 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00191 /  0.10 (10254)
  covalent geometry    : angle       0.43436 /  0.24 (14041)
  hydrogen bonds       : bond        0.04786 /  3.24 (  537)
  hydrogen bonds       : angle       3.76917 /  2.66 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 151
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8261 (mttt) cc_final: 0.7912 (mtmm)
REVERT: A  172 GLU cc_start: 0.8003 (tt0) cc_final: 0.7563 (mt-10)
REVERT: A  190 LYS cc_start: 0.7809 (tttt) cc_final: 0.7356 (ptpt)
REVERT: A  202 GLN cc_start: 0.7552 (mt0) cc_final: 0.7010 (mm110)
REVERT: A  220 LYS cc_start: 0.8581 (mttt) cc_final: 0.8278 (mmpt)
REVERT: A  239 LYS cc_start: 0.8250 (mttt) cc_final: 0.7664 (mmtm)
REVERT: A  393 GLU cc_start: 0.8156 (tt0) cc_final: 0.7924 (tp30)
REVERT: A  412 ARG cc_start: 0.8483 (ptt-90) cc_final: 0.7862 (ptt90)
REVERT: A  453 LYS cc_start: 0.8561 (mttp) cc_final: 0.8131 (mmpt)
REVERT: A  533 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7885 (tp30)
REVERT: A  558 ARG cc_start: 0.7685 (ttt-90) cc_final: 0.7230 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8329 (tttt) cc_final: 0.7560 (ttpp)
REVERT: A  574 ARG cc_start: 0.8381 (ttt180) cc_final: 0.7742 (ttm110)
REVERT: A  705 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7787 (mm-30)
REVERT: A  725 LYS cc_start: 0.8206 (mttt) cc_final: 0.7973 (mttp)
REVERT: A  794 GLN cc_start: 0.8347 (mt0) cc_final: 0.8085 (mp10)
REVERT: A  800 ARG cc_start: 0.8074 (ttp-110) cc_final: 0.7767 (tpm170)
REVERT: A  837 GLU cc_start: 0.7967 (tt0) cc_final: 0.7512 (tp30)
REVERT: A  841 LYS cc_start: 0.7632 (tttp) cc_final: 0.7096 (mtmt)
REVERT: A  867 LYS cc_start: 0.8263 (mttt) cc_final: 0.7614 (tttm)
REVERT: A 1029 LYS cc_start: 0.7587 (tttt) cc_final: 0.7242 (mppt)
REVERT: A 1068 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7528 (mp0)
REVERT: A 1070 LYS cc_start: 0.8247 (mttt) cc_final: 0.7877 (mtmt)
REVERT: A 1085 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8024 (mt-10)
  outliers start: 10
  outliers final: 7
  residues processed: 158
  average time/residue: 0.6791
  time to fit residues: 113.0180
Evaluate side-chains
  154 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 145
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue  927 SER
Chi-restraints excluded: chain A residue 1067 VAL
Chi-restraints excluded: chain A residue 1085 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 59 optimal weight:    0.5980
   chunk 20 optimal weight:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 60 optimal weight:    0.1980
   chunk 93 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  63 ASN
A  92 ASN
A 103 GLN
A 219 GLN
A 256 ASN
A 428 ASN
A 596 GLN
A 710 ASN
A 842 GLN
A1004 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.140491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.110831 restraints weight = 21024.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 2.20
r_work: 0.2964 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2719
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2719
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8964
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10254  Z= 0.109
  Angle     :  0.445   5.516  14041  Z= 0.246
  Chirality :  0.037   0.146   1559
  Planarity :  0.004   0.038   1613
  Dihedral  : 15.921 105.431   2044
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  9.13 %
    Favored  : 89.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.68 (0.25), residues: 1064
  helix:  2.55 (0.20), residues: 609
  sheet:  0.95 (0.76), residues: 50
  loop :  0.79 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 695 
 TYR   0.020   0.001   TYR A  17 
 PHE   0.015   0.001   PHE A 792 
 TRP   0.006   0.001   TRP A 724 
 HIS   0.004   0.001   HIS A 669 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00227 /  0.11 (10254)
  covalent geometry    : angle       0.44452 /  0.25 (14041)
  hydrogen bonds       : bond        0.04890 /  3.30 (  537)
  hydrogen bonds       : angle       3.75817 /  2.65 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 144
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8377 (mttt) cc_final: 0.8026 (mtmm)
REVERT: A  172 GLU cc_start: 0.8156 (tt0) cc_final: 0.7688 (mt-10)
REVERT: A  190 LYS cc_start: 0.7903 (tttt) cc_final: 0.7369 (ptpt)
REVERT: A  202 GLN cc_start: 0.7639 (mt0) cc_final: 0.7030 (mm110)
REVERT: A  220 LYS cc_start: 0.8574 (mttt) cc_final: 0.8219 (mmpt)
REVERT: A  239 LYS cc_start: 0.8342 (mttt) cc_final: 0.7725 (mmtm)
REVERT: A  393 GLU cc_start: 0.8377 (tt0) cc_final: 0.7991 (tp30)
REVERT: A  412 ARG cc_start: 0.8667 (ptt-90) cc_final: 0.7979 (ptt90)
REVERT: A  453 LYS cc_start: 0.8557 (mttp) cc_final: 0.8019 (mmpt)
REVERT: A  533 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7906 (tp30)
REVERT: A  558 ARG cc_start: 0.7884 (ttt-90) cc_final: 0.7294 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8412 (tttt) cc_final: 0.7613 (ttpp)
REVERT: A  574 ARG cc_start: 0.8519 (ttt180) cc_final: 0.7824 (ttm110)
REVERT: A  705 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7967 (mm-30)
REVERT: A  725 LYS cc_start: 0.8309 (mttt) cc_final: 0.8043 (mttp)
REVERT: A  794 GLN cc_start: 0.8585 (mt0) cc_final: 0.8312 (mp10)
REVERT: A  800 ARG cc_start: 0.8351 (ttp-110) cc_final: 0.7902 (tpm170)
REVERT: A  841 LYS cc_start: 0.7687 (tttp) cc_final: 0.7089 (mtmt)
REVERT: A  867 LYS cc_start: 0.8342 (mttt) cc_final: 0.7642 (tttm)
REVERT: A 1029 LYS cc_start: 0.7617 (tttt) cc_final: 0.7222 (mppt)
REVERT: A 1068 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7664 (mp0)
REVERT: A 1070 LYS cc_start: 0.8265 (mttt) cc_final: 0.7879 (mtmt)
  outliers start: 11
  outliers final: 8
  residues processed: 153
  average time/residue: 0.6952
  time to fit residues: 111.7232
Evaluate side-chains
  152 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 143
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue  927 SER
Chi-restraints excluded: chain A residue 1067 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 94 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0570
   chunk 57 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.7702

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  63 ASN
A 103 GLN
A 219 GLN
A 256 ASN
A 596 GLN
A 710 ASN
A 842 GLN
A 954 ASN
A1004 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.141886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.111938 restraints weight = 24439.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 2.49
r_work: 0.2944 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2959
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.2959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8927
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10254  Z= 0.111
  Angle     :  0.447   5.452  14041  Z= 0.247
  Chirality :  0.037   0.147   1559
  Planarity :  0.004   0.042   1613
  Dihedral  : 15.916 105.034   2044
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.13 %
    Favored  : 89.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.65 (0.25), residues: 1064
  helix:  2.55 (0.20), residues: 609
  sheet:  0.94 (0.84), residues: 44
  loop :  0.74 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 695 
 TYR   0.020   0.001   TYR A  17 
 PHE   0.016   0.001   PHE A 792 
 TRP   0.005   0.001   TRP A 724 
 HIS   0.004   0.001   HIS A 669 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.11 (10254)
  covalent geometry    : angle       0.44661 /  0.25 (14041)
  hydrogen bonds       : bond        0.04915 /  3.32 (  537)
  hydrogen bonds       : angle       3.75510 /  2.65 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 141
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8306 (mttt) cc_final: 0.7960 (mtmm)
REVERT: A  172 GLU cc_start: 0.8067 (tt0) cc_final: 0.7625 (mt-10)
REVERT: A  190 LYS cc_start: 0.7787 (tttt) cc_final: 0.7348 (ptpt)
REVERT: A  202 GLN cc_start: 0.7616 (mt0) cc_final: 0.7049 (mm110)
REVERT: A  220 LYS cc_start: 0.8584 (mttt) cc_final: 0.8282 (mmpt)
REVERT: A  239 LYS cc_start: 0.8281 (mttt) cc_final: 0.7722 (mmtm)
REVERT: A  393 GLU cc_start: 0.8241 (tt0) cc_final: 0.7979 (tp30)
REVERT: A  412 ARG cc_start: 0.8534 (ptt-90) cc_final: 0.7879 (ptt90)
REVERT: A  453 LYS cc_start: 0.8586 (mttp) cc_final: 0.8123 (mmpt)
REVERT: A  533 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7893 (tp30)
REVERT: A  558 ARG cc_start: 0.7733 (ttt-90) cc_final: 0.7246 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8390 (tttt) cc_final: 0.7637 (ttpp)
REVERT: A  574 ARG cc_start: 0.8437 (ttt180) cc_final: 0.7795 (ttm110)
REVERT: A  705 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7864 (mm-30)
REVERT: A  725 LYS cc_start: 0.8226 (mttt) cc_final: 0.7990 (mttp)
REVERT: A  794 GLN cc_start: 0.8390 (mt0) cc_final: 0.8139 (mp10)
REVERT: A  800 ARG cc_start: 0.8143 (ttp-110) cc_final: 0.7824 (tpm170)
REVERT: A  841 LYS cc_start: 0.7674 (tttp) cc_final: 0.7099 (mtmt)
REVERT: A  867 LYS cc_start: 0.8285 (mttt) cc_final: 0.7634 (tttm)
REVERT: A 1029 LYS cc_start: 0.7594 (tttt) cc_final: 0.7233 (mppt)
REVERT: A 1068 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7582 (mp0)
REVERT: A 1070 LYS cc_start: 0.8251 (mttt) cc_final: 0.7891 (mtmt)
  outliers start: 9
  outliers final: 8
  residues processed: 148
  average time/residue: 0.7241
  time to fit residues: 112.3995
Evaluate side-chains
  151 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 142
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue  927 SER
Chi-restraints excluded: chain A residue 1067 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9990
   chunk 81 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 86 optimal weight:    0.7980
   chunk 104 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  63 ASN
A 103 GLN
A 219 GLN
A 256 ASN
A 596 GLN
A 710 ASN
A 842 GLN
A1004 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.140286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.110809 restraints weight = 28559.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 2.76
r_work: 0.2907 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2795
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2795 r_free = 0.2795    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2794 r_free = 0.2794    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2794
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8936
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10254  Z= 0.114
  Angle     :  0.451   5.412  14041  Z= 0.249
  Chirality :  0.037   0.147   1559
  Planarity :  0.004   0.034   1613
  Dihedral  : 15.903 104.716   2044
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.44 %
    Favored  : 89.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.63 (0.25), residues: 1064
  helix:  2.53 (0.20), residues: 609
  sheet:  0.92 (0.84), residues: 44
  loop :  0.73 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 695 
 TYR   0.020   0.001   TYR A  17 
 PHE   0.016   0.001   PHE A 792 
 TRP   0.005   0.001   TRP A 724 
 HIS   0.004   0.001   HIS A 669 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.11 (10254)
  covalent geometry    : angle       0.45059 /  0.25 (14041)
  hydrogen bonds       : bond        0.04973 /  3.35 (  537)
  hydrogen bonds       : angle       3.75889 /  2.65 ( 1473)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3808.93 seconds
wall clock time: 65 minutes 31.91 seconds (3931.91 seconds total)