Starting phenix.real_space_refine
on Sun Jun  8 19:31:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wf8_37486/06_2025/8wf8_37486.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wf8_37486/06_2025/8wf8_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_37486/06_2025/8wf8_37486.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wf8_37486/06_2025/8wf8_37486.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wf8_37486/06_2025/8wf8_37486.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wf8_37486/06_2025/8wf8_37486.cif"
  }
  resolution = 2.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.18, per 1000 atoms: 1.02
  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: 2.31
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  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: 3.68
  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: 4.10

  Time building geometry restraints manager: 2.79 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=" O5'   A B  29 "
       pdb=" C5'   A B  29 "
    ideal  model  delta    sigma   weight residual
    1.424  1.472 -0.048 1.50e-02 4.44e+03 1.01e+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
  ... (remaining 10249 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.88: 12773
        2.88 -     5.76: 1138
        5.76 -     8.63: 117
        8.63 -    11.51: 10
       11.51 -    14.39: 3
  Bond angle restraints: 14041
  Sorted by residual:
  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 1.50e+00 4.44e-01 9.20e+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
  angle pdb=" C   ASP A 322 "
        pdb=" CA  ASP A 322 "
        pdb=" CB  ASP A 322 "
      ideal   model   delta    sigma   weight residual
     110.79   99.50   11.29 1.66e+00 3.63e-01 4.62e+01
  angle pdb=" CA BPHE A1003 "
        pdb=" CB BPHE A1003 "
        pdb=" CG BPHE A1003 "
      ideal   model   delta    sigma   weight residual
     113.80  120.06   -6.26 1.00e+00 1.00e+00 3.92e+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: 1335
       0.132 -    0.264: 214
       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:             1.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     34.280
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
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= 0.582
  Angle     :  1.722  14.390  14041  Z= 1.100
  Chirality :  0.093   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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.037   0.010   TRP A 724 
 HIS   0.010   0.004   HIS A 223 
 PHE   0.047   0.009   PHE A 819 
 TYR   0.068   0.009   TYR A 162 
 ARG   0.045   0.005   ARG A 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18374 (  537)
  hydrogen bonds       : angle       6.81719 ( 1473)
  covalent geometry    : bond        0.00957 (10254)
  covalent geometry    : angle       1.72186 (14041)

*********************** 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  : 1.005 
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: 0.6933 (mm-30)
REVERT: A  419 MET cc_start: 0.7134 (mtm) cc_final: 0.6819 (ttm)
REVERT: A  420 LYS cc_start: 0.7433 (mttt) cc_final: 0.6972 (mptp)
REVERT: A  497 LYS cc_start: 0.8690 (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: 0.8370 (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: 1.7880
  time to fit residues: 348.1383
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  : 1.114 
-------------------------------------------------------------------------------
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 93 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 44 optimal weight:   10.0000
   chunk 87 optimal weight:    0.0870
   chunk 33 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.7558

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

Flipped N/Q/H residues before XYZ refinement:
A  57 HIS
A  60 ASN
A  63 ASN
A  92 ASN
A 103 GLN
A 153 GLN
A 219 GLN
A 240 GLN
A 256 ASN
A 287 ASN
A 710 ASN
A 842 GLN
A 993 GLN
A1004 ASN
A1038 ASN
A1045 GLN
A1054 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.138673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.109881 restraints weight = 15812.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.73
r_work: 0.2995 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2744
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2744 r_free = 0.2744    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2744 r_free = 0.2744    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2744
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10254  Z= 0.128
  Angle     :  0.537   5.812  14041  Z= 0.292
  Chirality :  0.040   0.216   1559
  Planarity :  0.004   0.029   1613
  Dihedral  : 16.052 113.120   2045
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  6.22 %
    Favored  : 92.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.25), residues: 1064
  helix:  1.83 (0.20), residues: 606
  sheet: -0.11 (0.70), residues: 49
  loop :  0.63 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 724 
 HIS   0.005   0.001   HIS A 669 
 PHE   0.016   0.002   PHE A 792 
 TYR   0.019   0.002   TYR A 886 
 ARG   0.005   0.000   ARG A 579 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05516 (  537)
  hydrogen bonds       : angle       4.12440 ( 1473)
  covalent geometry    : bond        0.00263 (10254)
  covalent geometry    : angle       0.53672 (14041)

*********************** 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
  182 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 174
  time to evaluate  : 1.113 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8431 (mttt) cc_final: 0.7965 (mtmp)
REVERT: A  172 GLU cc_start: 0.8145 (tt0) cc_final: 0.7690 (mt-10)
REVERT: A  190 LYS cc_start: 0.7947 (tttt) cc_final: 0.7354 (ptpt)
REVERT: A  202 GLN cc_start: 0.7740 (mt0) cc_final: 0.7126 (mm110)
REVERT: A  220 LYS cc_start: 0.8634 (mttt) cc_final: 0.8220 (mmpt)
REVERT: A  221 LYS cc_start: 0.8334 (mttt) cc_final: 0.8044 (mmtm)
REVERT: A  239 LYS cc_start: 0.8389 (mttt) cc_final: 0.7748 (mmtm)
REVERT: A  278 LYS cc_start: 0.7988 (mttt) cc_final: 0.6928 (mptt)
REVERT: A  323 ASP cc_start: 0.7249 (p0) cc_final: 0.7007 (m-30)
REVERT: A  393 GLU cc_start: 0.8257 (tt0) cc_final: 0.7858 (tp30)
REVERT: A  412 ARG cc_start: 0.8631 (ptt-90) cc_final: 0.7928 (ptt90)
REVERT: A  419 MET cc_start: 0.7800 (mtm) cc_final: 0.7422 (mtm)
REVERT: A  420 LYS cc_start: 0.7928 (mttt) cc_final: 0.7688 (mptp)
REVERT: A  533 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7954 (tp30)
REVERT: A  558 ARG cc_start: 0.7891 (ttt-90) cc_final: 0.7258 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8423 (tttt) cc_final: 0.7643 (ttpp)
REVERT: A  574 ARG cc_start: 0.8442 (ttt180) cc_final: 0.7854 (ttm110)
REVERT: A  579 ARG cc_start: 0.8153 (mtp180) cc_final: 0.7945 (mtp180)
REVERT: A  657 LYS cc_start: 0.8593 (mmtp) cc_final: 0.7837 (mppt)
REVERT: A  705 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7975 (mm-30)
REVERT: A  725 LYS cc_start: 0.8341 (mttt) cc_final: 0.7866 (mptp)
REVERT: A  794 GLN cc_start: 0.8541 (mt0) cc_final: 0.8216 (mp10)
REVERT: A  800 ARG cc_start: 0.8355 (ttp-110) cc_final: 0.7961 (tpm170)
REVERT: A  816 GLN cc_start: 0.8522 (mt0) cc_final: 0.8087 (mm-40)
REVERT: A  837 GLU cc_start: 0.8121 (tt0) cc_final: 0.7623 (tp30)
REVERT: A  841 LYS cc_start: 0.7533 (tttp) cc_final: 0.7050 (mtmt)
REVERT: A  867 LYS cc_start: 0.8469 (mttt) cc_final: 0.7828 (tttt)
REVERT: A  972 GLU cc_start: 0.8132 (tp30) cc_final: 0.7921 (tt0)
REVERT: A  985 MET cc_start: 0.8663 (mtp) cc_final: 0.8423 (mtt)
REVERT: A 1029 LYS cc_start: 0.7742 (tttt) cc_final: 0.7378 (mptt)
REVERT: A 1068 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7664 (mp0)
REVERT: A 1070 LYS cc_start: 0.8375 (mttt) cc_final: 0.8016 (mtmt)
REVERT: A 1089 MET cc_start: 0.7740 (mmt) cc_final: 0.7536 (mmt)
  outliers start: 8
  outliers final: 3
  residues processed: 180
  average time/residue: 1.9091
  time to fit residues: 361.3086
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  : 1.434 
-------------------------------------------------------------------------------
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  834 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 62 optimal weight:    0.0980
   chunk 7 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 18 optimal weight:    0.4980
   chunk 34 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 103 GLN
A 171 ASN
A 219 GLN
A 240 GLN
A 596 GLN
A 710 ASN
A 842 GLN
A1038 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.138055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.108368 restraints weight = 22247.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 2.35
r_work: 0.2903 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2790
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8717
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10254  Z= 0.138
  Angle     :  0.516   5.621  14041  Z= 0.279
  Chirality :  0.040   0.191   1559
  Planarity :  0.004   0.031   1613
  Dihedral  : 15.997 110.876   2044
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  7.05 %
    Favored  : 91.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.37 (0.25), residues: 1064
  helix:  2.33 (0.20), residues: 607
  sheet:  0.36 (0.75), residues: 42
  loop :  0.67 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 724 
 HIS   0.005   0.001   HIS A 669 
 PHE   0.018   0.002   PHE A 792 
 TYR   0.021   0.002   TYR A  17 
 ARG   0.004   0.000   ARG A 579 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05482 (  537)
  hydrogen bonds       : angle       3.96969 ( 1473)
  covalent geometry    : bond        0.00302 (10254)
  covalent geometry    : angle       0.51649 (14041)

*********************** 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
  174 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 159
  time to evaluate  : 1.084 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8328 (mttt) cc_final: 0.7938 (mtmm)
REVERT: A  172 GLU cc_start: 0.8079 (tt0) cc_final: 0.7618 (mt-10)
REVERT: A  190 LYS cc_start: 0.7888 (tttt) cc_final: 0.7361 (ptpt)
REVERT: A  202 GLN cc_start: 0.7705 (mt0) cc_final: 0.7092 (mm110)
REVERT: A  220 LYS cc_start: 0.8630 (mttt) cc_final: 0.8290 (mmpt)
REVERT: A  221 LYS cc_start: 0.8355 (mttt) cc_final: 0.8083 (mmtm)
REVERT: A  239 LYS cc_start: 0.8237 (mttt) cc_final: 0.7628 (mmtm)
REVERT: A  248 ARG cc_start: 0.8640 (mmt180) cc_final: 0.8374 (mmt180)
REVERT: A  393 GLU cc_start: 0.8166 (tt0) cc_final: 0.7904 (tp30)
REVERT: A  412 ARG cc_start: 0.8517 (ptt-90) cc_final: 0.7883 (ptt90)
REVERT: A  420 LYS cc_start: 0.7854 (mttt) cc_final: 0.7547 (mptp)
REVERT: A  442 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8376 (mm-30)
REVERT: A  533 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7921 (tp30)
REVERT: A  558 ARG cc_start: 0.7768 (ttt-90) cc_final: 0.7271 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8371 (tttt) cc_final: 0.7611 (ttpp)
REVERT: A  574 ARG cc_start: 0.8410 (ttt180) cc_final: 0.7753 (ttm110)
REVERT: A  579 ARG cc_start: 0.7961 (mtp180) cc_final: 0.7752 (mtp180)
REVERT: A  657 LYS cc_start: 0.8547 (mmtp) cc_final: 0.7826 (mppt)
REVERT: A  705 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7841 (mm-30)
REVERT: A  725 LYS cc_start: 0.8304 (mttt) cc_final: 0.7907 (mptp)
REVERT: A  794 GLN cc_start: 0.8444 (mt0) cc_final: 0.8129 (mp10)
REVERT: A  800 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7825 (tpm170)
REVERT: A  816 GLN cc_start: 0.8415 (mt0) cc_final: 0.7982 (mm-40)
REVERT: A  841 LYS cc_start: 0.7575 (tttp) cc_final: 0.7070 (mtmt)
REVERT: A  867 LYS cc_start: 0.8363 (mttt) cc_final: 0.7674 (tttm)
REVERT: A  985 MET cc_start: 0.8605 (mtp) cc_final: 0.8368 (mtt)
REVERT: A 1029 LYS cc_start: 0.7619 (tttt) cc_final: 0.7312 (mptt)
REVERT: A 1068 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7566 (mp0)
REVERT: A 1070 LYS cc_start: 0.8326 (mttt) cc_final: 0.7901 (mtmt)
  outliers start: 15
  outliers final: 7
  residues processed: 169
  average time/residue: 1.8853
  time to fit residues: 335.0631
Evaluate side-chains
  160 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 152
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
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  737 SER
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 72 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 102 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0050
   chunk 48 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 20 optimal weight:    6.9990
   chunk 9 optimal weight:    0.0370
   overall best weight:    0.4874

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A  68 GLN
A  92 ASN
A 103 GLN
A 171 ASN
A 219 GLN
A 256 ASN
A 596 GLN
A 710 ASN
A 842 GLN
A1004 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.142803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.115558 restraints weight = 13647.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 1.37
r_work: 0.3072 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2844
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2844 r_free = 0.2844    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2844 r_free = 0.2844    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2844
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8675
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10254  Z= 0.099
  Angle     :  0.445   5.347  14041  Z= 0.240
  Chirality :  0.037   0.157   1559
  Planarity :  0.003   0.032   1613
  Dihedral  : 15.863 106.622   2044
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  8.30 %
    Favored  : 90.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.25), residues: 1064
  helix:  2.62 (0.20), residues: 609
  sheet:  0.76 (0.78), residues: 44
  loop :  0.73 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 724 
 HIS   0.003   0.001   HIS A 669 
 PHE   0.014   0.001   PHE A 792 
 TYR   0.017   0.001   TYR A  17 
 ARG   0.004   0.000   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04479 (  537)
  hydrogen bonds       : angle       3.72627 ( 1473)
  covalent geometry    : bond        0.00199 (10254)
  covalent geometry    : angle       0.44472 (14041)

*********************** 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
  166 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 157
  time to evaluate  : 1.054 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8241 (mttt) cc_final: 0.7975 (mtmm)
REVERT: A  172 GLU cc_start: 0.8073 (tt0) cc_final: 0.7612 (mt-10)
REVERT: A  190 LYS cc_start: 0.7809 (tttt) cc_final: 0.7381 (ptpt)
REVERT: A  202 GLN cc_start: 0.7588 (mt0) cc_final: 0.7014 (mm110)
REVERT: A  220 LYS cc_start: 0.8564 (mttt) cc_final: 0.8303 (mmpt)
REVERT: A  221 LYS cc_start: 0.8384 (mttt) cc_final: 0.8106 (mmtm)
REVERT: A  239 LYS cc_start: 0.8284 (mttt) cc_final: 0.7711 (mmtm)
REVERT: A  393 GLU cc_start: 0.8239 (tt0) cc_final: 0.7930 (tp30)
REVERT: A  412 ARG cc_start: 0.8626 (ptt-90) cc_final: 0.7977 (ptt90)
REVERT: A  420 LYS cc_start: 0.7800 (mttt) cc_final: 0.7570 (mptp)
REVERT: A  520 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8058 (mt-10)
REVERT: A  533 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7912 (tp30)
REVERT: A  558 ARG cc_start: 0.7751 (ttt-90) cc_final: 0.7247 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8384 (tttt) cc_final: 0.7641 (ttpp)
REVERT: A  574 ARG cc_start: 0.8472 (ttt180) cc_final: 0.7828 (ttm110)
REVERT: A  705 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7892 (mm-30)
REVERT: A  725 LYS cc_start: 0.8236 (mttt) cc_final: 0.7856 (mptp)
REVERT: A  794 GLN cc_start: 0.8475 (mt0) cc_final: 0.8180 (mp10)
REVERT: A  800 ARG cc_start: 0.8173 (ttp-110) cc_final: 0.7858 (tpm170)
REVERT: A  841 LYS cc_start: 0.7615 (tttp) cc_final: 0.7052 (mtmt)
REVERT: A  867 LYS cc_start: 0.8322 (mttt) cc_final: 0.7708 (tttm)
REVERT: A  908 ASP cc_start: 0.6700 (OUTLIER) cc_final: 0.6036 (t0)
REVERT: A 1029 LYS cc_start: 0.7618 (tttt) cc_final: 0.7235 (mppt)
REVERT: A 1068 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7567 (mp0)
REVERT: A 1070 LYS cc_start: 0.8263 (mttt) cc_final: 0.7892 (mtmt)
REVERT: A 1085 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8091 (mt-10)
  outliers start: 9
  outliers final: 6
  residues processed: 164
  average time/residue: 2.0388
  time to fit residues: 351.5023
Evaluate side-chains
  157 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 149
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
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  518 LYS
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  737 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 73 optimal weight:    3.9990
   chunk 110 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 100 optimal weight:    0.5980
   chunk 84 optimal weight:    3.9990
   overall best weight:    2.6986

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 103 GLN
A 219 GLN
A 428 ASN
A 549 HIS
A 596 GLN
A 710 ASN
A 842 GLN
A 954 ASN
A1004 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.135025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.105050 restraints weight = 21633.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 2.22
r_work: 0.2901 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2745
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2745 r_free = 0.2745    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2745 r_free = 0.2745    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2745
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8779
moved from start:          0.2058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.086  10254  Z= 0.247
  Angle     :  0.613   5.548  14041  Z= 0.328
  Chirality :  0.046   0.194   1559
  Planarity :  0.005   0.046   1613
  Dihedral  : 16.118 111.342   2043
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  7.88 %
    Favored  : 90.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.25), residues: 1064
  helix:  2.13 (0.20), residues: 604
  sheet:  0.42 (0.78), residues: 42
  loop :  0.71 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 829 
 HIS   0.007   0.002   HIS A 669 
 PHE   0.022   0.002   PHE A 792 
 TYR   0.025   0.002   TYR A  17 
 ARG   0.006   0.001   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06645 (  537)
  hydrogen bonds       : angle       4.09962 ( 1473)
  covalent geometry    : bond        0.00584 (10254)
  covalent geometry    : angle       0.61266 (14041)

*********************** 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
  163 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.974 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8401 (mttt) cc_final: 0.8004 (mtmm)
REVERT: A  172 GLU cc_start: 0.8047 (tt0) cc_final: 0.7635 (mt-10)
REVERT: A  190 LYS cc_start: 0.7869 (tttt) cc_final: 0.7347 (ptpt)
REVERT: A  202 GLN cc_start: 0.7769 (mt0) cc_final: 0.7119 (mm110)
REVERT: A  220 LYS cc_start: 0.8587 (mttt) cc_final: 0.8309 (mmpt)
REVERT: A  221 LYS cc_start: 0.8406 (mttt) cc_final: 0.8104 (mmtm)
REVERT: A  239 LYS cc_start: 0.8339 (mttt) cc_final: 0.7666 (mmtm)
REVERT: A  393 GLU cc_start: 0.8214 (tt0) cc_final: 0.7893 (tp30)
REVERT: A  412 ARG cc_start: 0.8487 (ptt-90) cc_final: 0.7871 (ptt90)
REVERT: A  420 LYS cc_start: 0.7823 (mttt) cc_final: 0.7583 (mptp)
REVERT: A  533 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7876 (tp30)
REVERT: A  558 ARG cc_start: 0.7871 (ttt-90) cc_final: 0.7333 (ttp-110)
REVERT: A  570 ARG cc_start: 0.8263 (ttm110) cc_final: 0.8048 (ttm110)
REVERT: A  573 LYS cc_start: 0.8398 (tttt) cc_final: 0.7622 (ttpp)
REVERT: A  574 ARG cc_start: 0.8487 (ttt180) cc_final: 0.7833 (ttm110)
REVERT: A  589 MET cc_start: 0.8888 (ttt) cc_final: 0.8453 (ttt)
REVERT: A  705 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7847 (mm-30)
REVERT: A  725 LYS cc_start: 0.8321 (mttt) cc_final: 0.8050 (mttp)
REVERT: A  794 GLN cc_start: 0.8399 (mt0) cc_final: 0.8115 (mp10)
REVERT: A  800 ARG cc_start: 0.8197 (ttp-110) cc_final: 0.7863 (tpm170)
REVERT: A  841 LYS cc_start: 0.7744 (tttp) cc_final: 0.7186 (mtmt)
REVERT: A  867 LYS cc_start: 0.8388 (mttt) cc_final: 0.7750 (tttt)
REVERT: A 1029 LYS cc_start: 0.7665 (tttt) cc_final: 0.7366 (mptt)
REVERT: A 1068 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7662 (mp0)
REVERT: A 1070 LYS cc_start: 0.8365 (mttt) cc_final: 0.7957 (mtmt)
  outliers start: 16
  outliers final: 10
  residues processed: 158
  average time/residue: 1.8107
  time to fit residues: 300.8048
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  : 1.021 
-------------------------------------------------------------------------------
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  518 LYS
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  737 SER
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  927 SER
Chi-restraints excluded: chain A residue 1067 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0670
   chunk 79 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 67 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0670
   overall best weight:    0.4856

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 103 GLN
A 171 ASN
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 = 0.3523 r_free = 0.3523 target = 0.143367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.113840 restraints weight = 25972.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.61
r_work: 0.2935 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2821
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2821 r_free = 0.2821    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2821 r_free = 0.2821    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2821
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10254  Z= 0.100
  Angle     :  0.444   5.330  14041  Z= 0.239
  Chirality :  0.036   0.151   1559
  Planarity :  0.003   0.034   1613
  Dihedral  : 15.796 104.875   2043
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  8.40 %
    Favored  : 90.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.63 (0.25), residues: 1064
  helix:  2.55 (0.20), residues: 609
  sheet:  0.53 (0.82), residues: 42
  loop :  0.75 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 724 
 HIS   0.003   0.001   HIS A 669 
 PHE   0.014   0.001   PHE A 792 
 TYR   0.018   0.001   TYR A  17 
 ARG   0.005   0.000   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04547 (  537)
  hydrogen bonds       : angle       3.74593 ( 1473)
  covalent geometry    : bond        0.00204 (10254)
  covalent geometry    : angle       0.44419 (14041)

*********************** 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
  160 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 149
  time to evaluate  : 1.314 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8306 (mttt) cc_final: 0.8023 (mtmm)
REVERT: A  172 GLU cc_start: 0.8038 (tt0) cc_final: 0.7571 (mt-10)
REVERT: A  190 LYS cc_start: 0.7791 (tttt) cc_final: 0.7338 (ptpt)
REVERT: A  202 GLN cc_start: 0.7672 (mt0) cc_final: 0.7034 (mm110)
REVERT: A  220 LYS cc_start: 0.8621 (mttt) cc_final: 0.8316 (mmpt)
REVERT: A  221 LYS cc_start: 0.8454 (mttt) cc_final: 0.8099 (mmtm)
REVERT: A  239 LYS cc_start: 0.8291 (mttt) cc_final: 0.7724 (mmtm)
REVERT: A  393 GLU cc_start: 0.8240 (tt0) cc_final: 0.7930 (tp30)
REVERT: A  412 ARG cc_start: 0.8574 (ptt-90) cc_final: 0.7929 (ptt90)
REVERT: A  420 LYS cc_start: 0.7729 (mttt) cc_final: 0.7344 (tttm)
REVERT: A  533 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7926 (tp30)
REVERT: A  558 ARG cc_start: 0.7793 (ttt-90) cc_final: 0.7287 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8397 (tttt) cc_final: 0.7644 (ttpp)
REVERT: A  574 ARG cc_start: 0.8486 (ttt180) cc_final: 0.7785 (ttm110)
REVERT: A  705 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7878 (mm-30)
REVERT: A  725 LYS cc_start: 0.8283 (mttt) cc_final: 0.7955 (mptp)
REVERT: A  794 GLN cc_start: 0.8442 (mt0) cc_final: 0.8187 (mp10)
REVERT: A  800 ARG cc_start: 0.8162 (ttp-110) cc_final: 0.7834 (tpm170)
REVERT: A  841 LYS cc_start: 0.7703 (tttp) cc_final: 0.7090 (mtmt)
REVERT: A  867 LYS cc_start: 0.8325 (mttt) cc_final: 0.7647 (tttm)
REVERT: A  942 LYS cc_start: 0.8528 (tttp) cc_final: 0.8308 (mttt)
REVERT: A 1007 LYS cc_start: 0.7791 (tttp) cc_final: 0.7431 (tttp)
REVERT: A 1029 LYS cc_start: 0.7639 (tttt) cc_final: 0.7190 (mppt)
REVERT: A 1068 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7606 (mp0)
REVERT: A 1070 LYS cc_start: 0.8259 (mttt) cc_final: 0.7874 (mtmt)
REVERT: A 1085 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8053 (mt-10)
  outliers start: 11
  outliers final: 8
  residues processed: 156
  average time/residue: 1.8978
  time to fit residues: 313.0031
Evaluate side-chains
  159 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 150
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
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  518 LYS
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  737 SER
Chi-restraints excluded: chain A residue  927 SER
Chi-restraints excluded: chain A residue 1067 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 71 optimal weight:    5.9990
   chunk 73 optimal weight:    0.6980
   chunk 59 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0370
   chunk 25 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A  63 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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.142823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.112741 restraints weight = 24977.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 2.58
r_work: 0.2940 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2973
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2973 r_free = 0.2973    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2973 r_free = 0.2973    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2973
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10254  Z= 0.105
  Angle     :  0.446   5.269  14041  Z= 0.240
  Chirality :  0.037   0.146   1559
  Planarity :  0.003   0.033   1613
  Dihedral  : 15.815 104.520   2043
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  8.61 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.68 (0.25), residues: 1064
  helix:  2.59 (0.20), residues: 610
  sheet:  0.57 (0.83), residues: 42
  loop :  0.75 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 724 
 HIS   0.003   0.001   HIS A 669 
 PHE   0.016   0.001   PHE A 792 
 TYR   0.019   0.001   TYR A  17 
 ARG   0.005   0.000   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04649 (  537)
  hydrogen bonds       : angle       3.70076 ( 1473)
  covalent geometry    : bond        0.00220 (10254)
  covalent geometry    : angle       0.44607 (14041)

*********************** 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
  160 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 149
  time to evaluate  : 1.107 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.8001 (tt0) cc_final: 0.7549 (mt-10)
REVERT: A  190 LYS cc_start: 0.7717 (tttt) cc_final: 0.7310 (ptpt)
REVERT: A  202 GLN cc_start: 0.7634 (mt0) cc_final: 0.7022 (mm110)
REVERT: A  220 LYS cc_start: 0.8607 (mttt) cc_final: 0.8342 (mmpt)
REVERT: A  221 LYS cc_start: 0.8492 (mttt) cc_final: 0.8109 (mmtm)
REVERT: A  239 LYS cc_start: 0.8256 (mttt) cc_final: 0.7701 (mmtm)
REVERT: A  393 GLU cc_start: 0.8217 (tt0) cc_final: 0.7939 (tp30)
REVERT: A  412 ARG cc_start: 0.8584 (ptt-90) cc_final: 0.7917 (ptt90)
REVERT: A  420 LYS cc_start: 0.7696 (mttt) cc_final: 0.7358 (tttm)
REVERT: A  533 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7911 (tp30)
REVERT: A  558 ARG cc_start: 0.7749 (ttt-90) cc_final: 0.7259 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8369 (tttt) cc_final: 0.7616 (ttpp)
REVERT: A  574 ARG cc_start: 0.8492 (ttt180) cc_final: 0.7820 (ttm110)
REVERT: A  705 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7845 (mm-30)
REVERT: A  710 ASN cc_start: 0.8272 (m-40) cc_final: 0.8072 (m110)
REVERT: A  725 LYS cc_start: 0.8274 (mttt) cc_final: 0.7946 (mptp)
REVERT: A  794 GLN cc_start: 0.8407 (mt0) cc_final: 0.8160 (mp10)
REVERT: A  800 ARG cc_start: 0.8143 (ttp-110) cc_final: 0.7825 (tpm170)
REVERT: A  841 LYS cc_start: 0.7717 (tttp) cc_final: 0.7106 (mtmt)
REVERT: A  867 LYS cc_start: 0.8316 (mttt) cc_final: 0.7669 (tttm)
REVERT: A  942 LYS cc_start: 0.8523 (tttp) cc_final: 0.8295 (mttt)
REVERT: A 1007 LYS cc_start: 0.7792 (tttp) cc_final: 0.7507 (tttp)
REVERT: A 1029 LYS cc_start: 0.7644 (tttt) cc_final: 0.7205 (mppt)
REVERT: A 1068 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7571 (mp0)
REVERT: A 1070 LYS cc_start: 0.8229 (mttt) cc_final: 0.7868 (mtmt)
REVERT: A 1085 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8074 (mt-10)
  outliers start: 11
  outliers final: 8
  residues processed: 157
  average time/residue: 2.0154
  time to fit residues: 334.5552
Evaluate side-chains
  156 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 147
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
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  737 SER
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 87 optimal weight:    0.1980
   chunk 88 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 103 GLN
A 219 GLN
A 596 GLN
A 842 GLN
A1004 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.138659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.108755 restraints weight = 21591.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 2.23
r_work: 0.2931 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2965
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8711
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10254  Z= 0.141
  Angle     :  0.491   5.416  14041  Z= 0.264
  Chirality :  0.039   0.147   1559
  Planarity :  0.004   0.044   1613
  Dihedral  : 15.863 105.793   2043
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  8.82 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (0.25), residues: 1064
  helix:  2.45 (0.20), residues: 609
  sheet:  0.50 (0.82), residues: 42
  loop :  0.72 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 724 
 HIS   0.005   0.001   HIS A 669 
 PHE   0.017   0.002   PHE A 792 
 TYR   0.022   0.002   TYR A  17 
 ARG   0.005   0.000   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05298 (  537)
  hydrogen bonds       : angle       3.82649 ( 1473)
  covalent geometry    : bond        0.00317 (10254)
  covalent geometry    : angle       0.49080 (14041)

*********************** 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
  157 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.7956 (ttmm) cc_final: 0.7131 (mptt)
REVERT: A  172 GLU cc_start: 0.8013 (tt0) cc_final: 0.7601 (mt-10)
REVERT: A  190 LYS cc_start: 0.7693 (tttt) cc_final: 0.7321 (ptpt)
REVERT: A  202 GLN cc_start: 0.7664 (mt0) cc_final: 0.7048 (mm110)
REVERT: A  220 LYS cc_start: 0.8608 (mttt) cc_final: 0.8369 (mmpt)
REVERT: A  221 LYS cc_start: 0.8471 (mttt) cc_final: 0.8119 (mmtm)
REVERT: A  239 LYS cc_start: 0.8276 (mttt) cc_final: 0.7717 (mmtm)
REVERT: A  393 GLU cc_start: 0.8175 (tt0) cc_final: 0.7936 (tp30)
REVERT: A  412 ARG cc_start: 0.8488 (ptt-90) cc_final: 0.7848 (ptt90)
REVERT: A  420 LYS cc_start: 0.7745 (mttt) cc_final: 0.7391 (tttm)
REVERT: A  533 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7878 (tp30)
REVERT: A  558 ARG cc_start: 0.7700 (ttt-90) cc_final: 0.7248 (ttp-110)
REVERT: A  570 ARG cc_start: 0.8231 (ttm110) cc_final: 0.8017 (ttm110)
REVERT: A  573 LYS cc_start: 0.8361 (tttt) cc_final: 0.7594 (ttpp)
REVERT: A  574 ARG cc_start: 0.8449 (ttt180) cc_final: 0.7777 (ttm110)
REVERT: A  705 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7797 (mm-30)
REVERT: A  725 LYS cc_start: 0.8281 (mttt) cc_final: 0.7971 (mptp)
REVERT: A  794 GLN cc_start: 0.8337 (mt0) cc_final: 0.8080 (mp10)
REVERT: A  800 ARG cc_start: 0.8107 (ttp-110) cc_final: 0.7810 (tpm170)
REVERT: A  841 LYS cc_start: 0.7719 (tttp) cc_final: 0.7142 (mtmt)
REVERT: A  867 LYS cc_start: 0.8338 (mttt) cc_final: 0.7688 (tttt)
REVERT: A  942 LYS cc_start: 0.8578 (tttp) cc_final: 0.8338 (mttt)
REVERT: A 1029 LYS cc_start: 0.7632 (tttt) cc_final: 0.7218 (mppt)
REVERT: A 1068 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7578 (mp0)
REVERT: A 1070 LYS cc_start: 0.8252 (mttt) cc_final: 0.7887 (mtmt)
REVERT: A 1085 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8008 (mt-10)
  outliers start: 13
  outliers final: 9
  residues processed: 153
  average time/residue: 1.8028
  time to fit residues: 289.7920
Evaluate side-chains
  155 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 145
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
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  737 SER
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue  927 SER
Chi-restraints excluded: chain A residue  941 LYS
Chi-restraints excluded: chain A residue 1067 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 93 optimal weight:    0.7980
   chunk 83 optimal weight:    9.9990
   chunk 86 optimal weight:    2.9990
   chunk 99 optimal weight:    4.9990
   chunk 104 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 101 optimal weight:    7.9990
   chunk 72 optimal weight:    0.2980
   chunk 0 optimal weight:    7.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
A  63 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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.137063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.107333 restraints weight = 24884.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 2.46
r_work: 0.2895 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2752
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2752 r_free = 0.2752    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2752 r_free = 0.2752    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2752
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.2305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  10254  Z= 0.168
  Angle     :  0.526   5.441  14041  Z= 0.282
  Chirality :  0.041   0.160   1559
  Planarity :  0.004   0.041   1613
  Dihedral  : 15.864 107.200   2043
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  8.40 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.25), residues: 1064
  helix:  2.29 (0.20), residues: 608
  sheet:  0.38 (0.81), residues: 42
  loop :  0.69 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 724 
 HIS   0.005   0.001   HIS A 669 
 PHE   0.019   0.002   PHE A 792 
 TYR   0.023   0.002   TYR A  17 
 ARG   0.005   0.000   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05729 (  537)
  hydrogen bonds       : angle       3.91929 ( 1473)
  covalent geometry    : bond        0.00385 (10254)
  covalent geometry    : angle       0.52591 (14041)

*********************** 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
  157 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 1.057 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7222 (mptt)
REVERT: A  172 GLU cc_start: 0.8076 (tt0) cc_final: 0.7663 (mt-10)
REVERT: A  190 LYS cc_start: 0.7766 (tttt) cc_final: 0.7331 (ptpt)
REVERT: A  202 GLN cc_start: 0.7743 (mt0) cc_final: 0.7073 (mm110)
REVERT: A  220 LYS cc_start: 0.8605 (mttt) cc_final: 0.8326 (mmpt)
REVERT: A  221 LYS cc_start: 0.8488 (mttt) cc_final: 0.8122 (mmtm)
REVERT: A  239 LYS cc_start: 0.8333 (mttt) cc_final: 0.7754 (mmtm)
REVERT: A  393 GLU cc_start: 0.8254 (tt0) cc_final: 0.7963 (tp30)
REVERT: A  412 ARG cc_start: 0.8531 (ptt-90) cc_final: 0.7913 (ptt90)
REVERT: A  420 LYS cc_start: 0.7740 (mttt) cc_final: 0.7338 (tttm)
REVERT: A  533 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7890 (tp30)
REVERT: A  558 ARG cc_start: 0.7910 (ttt-90) cc_final: 0.7354 (ttp-110)
REVERT: A  570 ARG cc_start: 0.8290 (ttm110) cc_final: 0.8077 (ttm110)
REVERT: A  573 LYS cc_start: 0.8389 (tttt) cc_final: 0.7618 (ttpp)
REVERT: A  574 ARG cc_start: 0.8507 (ttt180) cc_final: 0.7820 (ttm110)
REVERT: A  705 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7843 (mm-30)
REVERT: A  725 LYS cc_start: 0.8306 (mttt) cc_final: 0.7975 (mptp)
REVERT: A  794 GLN cc_start: 0.8436 (mt0) cc_final: 0.8176 (mp10)
REVERT: A  800 ARG cc_start: 0.8220 (ttp-110) cc_final: 0.7877 (tpm170)
REVERT: A  841 LYS cc_start: 0.7765 (tttp) cc_final: 0.7174 (mtmt)
REVERT: A  867 LYS cc_start: 0.8408 (mttt) cc_final: 0.7754 (tttt)
REVERT: A 1029 LYS cc_start: 0.7658 (tttt) cc_final: 0.7365 (mptt)
REVERT: A 1068 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7650 (mp0)
REVERT: A 1070 LYS cc_start: 0.8286 (mttt) cc_final: 0.7888 (mtmt)
  outliers start: 13
  outliers final: 9
  residues processed: 154
  average time/residue: 2.1719
  time to fit residues: 351.4578
Evaluate side-chains
  153 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 142
  time to evaluate  : 1.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue   34 LYS
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  737 SER
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 83 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0040
   chunk 9 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0040
   chunk 43 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.5804

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

Flipped N/Q/H residues before XYZ refinement:
A  63 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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.141027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.111445 restraints weight = 22279.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 2.29
r_work: 0.2955 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2998
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2998 r_free = 0.2998    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2998 r_free = 0.2998    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2998
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.2555

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= 0.104
  Angle     :  0.448   5.503  14041  Z= 0.242
  Chirality :  0.037   0.151   1559
  Planarity :  0.004   0.049   1613
  Dihedral  : 15.681 104.410   2043
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  8.92 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.58 (0.25), residues: 1064
  helix:  2.53 (0.20), residues: 609
  sheet:  0.41 (0.83), residues: 42
  loop :  0.71 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 724 
 HIS   0.003   0.001   HIS A 669 
 PHE   0.015   0.001   PHE A 792 
 TYR   0.019   0.001   TYR A  17 
 ARG   0.005   0.000   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04698 (  537)
  hydrogen bonds       : angle       3.74142 ( 1473)
  covalent geometry    : bond        0.00216 (10254)
  covalent geometry    : angle       0.44804 (14041)

********************** 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
  158 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 1.022 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7012 (mptt)
REVERT: A  172 GLU cc_start: 0.7921 (tt0) cc_final: 0.7489 (mt-10)
REVERT: A  190 LYS cc_start: 0.7680 (tttt) cc_final: 0.7330 (ptpt)
REVERT: A  202 GLN cc_start: 0.7649 (mt0) cc_final: 0.7040 (mm110)
REVERT: A  220 LYS cc_start: 0.8600 (mttt) cc_final: 0.8362 (mmpt)
REVERT: A  221 LYS cc_start: 0.8472 (mttt) cc_final: 0.8094 (mmtm)
REVERT: A  239 LYS cc_start: 0.8245 (mttt) cc_final: 0.7696 (mmtm)
REVERT: A  393 GLU cc_start: 0.8171 (tt0) cc_final: 0.7919 (tp30)
REVERT: A  412 ARG cc_start: 0.8497 (ptt-90) cc_final: 0.7864 (ptt90)
REVERT: A  420 LYS cc_start: 0.7632 (mttt) cc_final: 0.7281 (tttm)
REVERT: A  533 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7893 (tp30)
REVERT: A  558 ARG cc_start: 0.7768 (ttt-90) cc_final: 0.7311 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8366 (tttt) cc_final: 0.7601 (ttpp)
REVERT: A  574 ARG cc_start: 0.8429 (ttt180) cc_final: 0.7748 (ttm110)
REVERT: A  705 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7812 (mm-30)
REVERT: A  725 LYS cc_start: 0.8206 (mttt) cc_final: 0.7906 (mptp)
REVERT: A  794 GLN cc_start: 0.8351 (mt0) cc_final: 0.8109 (mp10)
REVERT: A  800 ARG cc_start: 0.8090 (ttp-110) cc_final: 0.7789 (tpm170)
REVERT: A  841 LYS cc_start: 0.7761 (tttp) cc_final: 0.7114 (mtmt)
REVERT: A  867 LYS cc_start: 0.8280 (mttt) cc_final: 0.7618 (tttm)
REVERT: A  942 LYS cc_start: 0.8568 (tttp) cc_final: 0.8323 (mttt)
REVERT: A 1029 LYS cc_start: 0.7626 (tttt) cc_final: 0.7338 (mptt)
REVERT: A 1068 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7564 (mp0)
REVERT: A 1070 LYS cc_start: 0.8231 (mttt) cc_final: 0.7861 (mtmt)
REVERT: A 1085 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7999 (mt-10)
  outliers start: 12
  outliers final: 9
  residues processed: 155
  average time/residue: 1.8358
  time to fit residues: 299.8288
Evaluate side-chains
  157 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 146
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue   34 LYS
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  737 SER
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 110 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0570
   chunk 0 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   chunk 51 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    1.2104

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

Flipped N/Q/H residues before XYZ refinement:
A  63 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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.139200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.110317 restraints weight = 15650.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.60
r_work: 0.2989 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2872 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2747
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2747
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8759
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10254  Z= 0.139
  Angle     :  0.488   5.593  14041  Z= 0.262
  Chirality :  0.039   0.146   1559
  Planarity :  0.004   0.039   1613
  Dihedral  : 15.731 105.086   2043
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  8.92 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.25), residues: 1064
  helix:  2.42 (0.20), residues: 609
  sheet:  0.39 (0.82), residues: 42
  loop :  0.70 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  50 
 HIS   0.005   0.001   HIS A 669 
 PHE   0.018   0.001   PHE A 792 
 TYR   0.022   0.002   TYR A  17 
 ARG   0.006   0.000   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05221 (  537)
  hydrogen bonds       : angle       3.82285 ( 1473)
  covalent geometry    : bond        0.00313 (10254)
  covalent geometry    : angle       0.48832 (14041)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9064.57 seconds
wall clock time: 157 minutes 38.35 seconds (9458.35 seconds total)