Starting phenix.real_space_refine
on Thu Feb  5 02:02:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ia0_52777/02_2026/9ia0_52777.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ia0_52777/02_2026/9ia0_52777.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ia0_52777/02_2026/9ia0_52777.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ia0_52777/02_2026/9ia0_52777.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ia0_52777/02_2026/9ia0_52777.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ia0_52777/02_2026/9ia0_52777.cif"
  }
  resolution = 2.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    4531      2.51       5
     N    1246      2.21       5
     O    1413      1.98       5
     H    6849      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14067
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 11620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 740, 11620
          Classifications: {'peptide': 740}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 710}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2447
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 2447
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 8, 'TRANS': 145}
  Time building chain proxies: 2.53, per 1000 atoms: 0.18
  Number of scatterers: 14067
  At special positions: 0
  Unit cell: (102.34, 81.141, 107.457, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     O    1413      8.00
     N    1246      7.00
     C    4531      6.00
     H    6849      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  31 " - pdb=" SG  CYS A 724 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 173 " - pdb=" SG  CYS A 725 " distance=2.06

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Conformation dependent library (CDL) restraints added in 409.2 milliseconds
  

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1674

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 5 sheets defined
      13.3% alpha, 54.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 32
    Processing helix  chain 'A' and resid 295 through 302
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 463 through 468
    Processing helix  chain 'A' and resid 537 through 542
    Processing helix  chain 'A' and resid 660 through 668
    Processing helix  chain 'A' and resid 669 through 674
    Processing helix  chain 'A' and resid 675 through 680
      removed outlier: 4.395A  pdb=" N   ASN A 680 " --> pdb=" O   GLU A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 773
    Processing helix  chain 'B' and resid 30 through 33
    Processing helix  chain 'B' and resid 45 through 58
      removed outlier: 3.501A  pdb=" N   ASN B  58 " --> pdb=" O   GLN B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 172
      removed outlier: 3.515A  pdb=" N   ASP B 149 " --> pdb=" O   LYS B 145 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU B 159 " --> pdb=" O   LEU B 155 " (cutoff:3.500A)
      Proline residue:  B 160  - end of helix
      removed outlier: 3.538A  pdb=" N   ASP B 170 " --> pdb=" O   ASP B 166 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 60
      removed outlier: 4.751A  pdb=" N   ILE A  54 " --> pdb=" O   ASP A  74 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   ASP A  74 " --> pdb=" O   ILE A  54 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   ALA A  56 " --> pdb=" O   SER A  72 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   SER A  72 " --> pdb=" O   ALA A  56 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   ASP A  85 " --> pdb=" O   GLY A  71 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   VAL A  73 " --> pdb=" O   GLN A  83 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   GLN A  83 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   ILE A  75 " --> pdb=" O   ARG A  81 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ARG A  81 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   SER A  80 " --> pdb=" O   ASP A 113 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   ASP A 113 " --> pdb=" O   SER A  80 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   LEU A  82 " --> pdb=" O   HIS A 111 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   HIS A 111 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   ALA A  84 " --> pdb=" O   ASN A 109 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   ASN A 109 " --> pdb=" O   ALA A  84 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASP A 105 " --> pdb=" O   GLN A  88 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   VAL A 104 " --> pdb=" O   ASN A 127 " (cutoff:3.500A)
      removed outlier: 5.532A  pdb=" N   ASN A 127 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   ALA A 106 " --> pdb=" O   TRP A 125 " (cutoff:3.500A)
      removed outlier: 5.494A  pdb=" N   TRP A 125 " --> pdb=" O   ALA A 106 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   GLY A 108 " --> pdb=" O   LYS A 123 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   LYS A 123 " --> pdb=" O   GLY A 108 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   LYS A 123 " --> pdb=" O   TRP A 136 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU A 153 " --> pdb=" O   ASP A 166 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLU A 186 " --> pdb=" O   TRP A 199 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL A 195 " --> pdb=" O   ASP A 190 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 150
      removed outlier: 4.392A  pdb=" N   LYS A 123 " --> pdb=" O   TRP A 136 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU A 153 " --> pdb=" O   ASP A 166 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLU A 186 " --> pdb=" O   TRP A 199 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL A 195 " --> pdb=" O   ASP A 190 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ARG A 202 " --> pdb=" O   TYR A 212 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   TYR A 212 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   LYS A 204 " --> pdb=" O   ILE A 210 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ILE A 210 " --> pdb=" O   LYS A 204 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 247 through 252
      removed outlier: 7.160A  pdb=" N   MET A 255 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   VAL A 747 " --> pdb=" O   ASN A 737 " (cutoff:3.500A)
      removed outlier: 8.247A  pdb=" N   ALA A 713 " --> pdb=" O   LEU A 736 " (cutoff:3.500A)
      removed outlier: 13.085A  pdb=" N   GLY A 738 " --> pdb=" O   LYS A 711 " (cutoff:3.500A)
      removed outlier: 13.103A  pdb=" N   LYS A 711 " --> pdb=" O   GLY A 738 " (cutoff:3.500A)
      removed outlier: 5.728A  pdb=" N   GLN A 712 " --> pdb=" O   ASP A 706 " (cutoff:3.500A)
      removed outlier: 5.599A  pdb=" N   ASP A 706 " --> pdb=" O   GLN A 712 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASP A 714 " --> pdb=" O   TYR A 704 " (cutoff:3.500A)
      removed outlier: 5.850A  pdb=" N   VAL A 635 " --> pdb=" O   ASP A 629 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   ASP A 629 " --> pdb=" O   VAL A 635 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR A 637 " --> pdb=" O   GLN A 627 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   SER A 605 " --> pdb=" O   TYR A 584 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   TYR A 584 " --> pdb=" O   SER A 605 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   VAL A 607 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 252
      removed outlier: 7.160A  pdb=" N   MET A 255 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   GLU A 275 " --> pdb=" O   THR A 258 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ASN A 274 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   LEU A 289 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   THR A 356 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
      removed outlier: 9.085A  pdb=" N   VAL A 334 " --> pdb=" O   TYR A 354 " (cutoff:3.500A)
      removed outlier: 10.962A  pdb=" N   TYR A 354 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 8.153A  pdb=" N   LYS A 375 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 5.278A  pdb=" N   GLU A 391 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 8.126A  pdb=" N   PHE A 377 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   SER A 389 " --> pdb=" O   PHE A 377 " (cutoff:3.500A)
      removed outlier: 5.473A  pdb=" N   ALA A 390 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   VAL A 418 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   PHE A 406 " --> pdb=" O   ASP A 402 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 63
      removed outlier: 4.059A  pdb=" N   LEU B  38 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
      removed outlier: 8.373A  pdb=" N   LEU B  75 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   ILE B  37 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   LEU B  77 " --> pdb=" O   ILE B  37 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   ASP B  39 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 9.020A  pdb=" N   LYS B  79 " --> pdb=" O   ASP B  39 " (cutoff:3.500A)
      removed outlier: 5.511A  pdb=" N   ASN B 105 " --> pdb=" O   GLY B  78 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   VAL B  80 " --> pdb=" O   THR B 103 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   THR B 103 " --> pdb=" O   VAL B  80 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   ILE B  82 " --> pdb=" O   ILE B 101 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   ILE B 101 " --> pdb=" O   ILE B  82 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   LYS B  84 " --> pdb=" O   GLN B  99 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   GLN B  99 " --> pdb=" O   LYS B  84 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   THR B  86 " --> pdb=" O   GLU B  97 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   GLU B  97 " --> pdb=" O   THR B  86 " (cutoff:3.500A)

    407 hydrogen bonds defined for protein.
    1125 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.93

  Time building geometry restraints manager: 1.49 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 6848
        1.12 -     1.30: 1277
        1.30 -     1.47: 2944
        1.47 -     1.65: 3118
        1.65 -     1.82: 51
  Bond restraints: 14238
  Sorted by residual:
  bond pdb=" NH1 ARG A 429 "
       pdb="HH11 ARG A 429 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.75e+01
  bond pdb=" CE1 TYR A 399 "
       pdb=" HE1 TYR A 399 "
    ideal  model  delta    sigma   weight residual
    0.930  1.082 -0.152 2.00e-02 2.50e+03 5.75e+01
  bond pdb=" CE1 HIS A 457 "
       pdb=" HE1 HIS A 457 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.74e+01
  bond pdb=" N   ASP A 342 "
       pdb=" H   ASP A 342 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" CE1 PHE A 241 "
       pdb=" HE1 PHE A 241 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.73e+01
  ... (remaining 14233 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 20692
        2.33 -     4.67: 3781
        4.67 -     7.00: 915
        7.00 -     9.34: 122
        9.34 -    11.67: 1
  Bond angle restraints: 25511
  Sorted by residual:
  angle pdb=" C   ILE A 164 "
        pdb=" CA  ILE A 164 "
        pdb=" CB  ILE A 164 "
      ideal   model   delta    sigma   weight residual
     110.28  118.04   -7.76 1.58e+00 4.01e-01 2.41e+01
  angle pdb=" CA  ILE A 230 "
        pdb=" C   ILE A 230 "
        pdb=" N   PRO A 231 "
      ideal   model   delta    sigma   weight residual
     116.57  121.36   -4.79 9.80e-01 1.04e+00 2.39e+01
  angle pdb=" CA  ASP A  26 "
        pdb=" CB  ASP A  26 "
        pdb=" CG  ASP A  26 "
      ideal   model   delta    sigma   weight residual
     112.60  117.37   -4.77 1.00e+00 1.00e+00 2.27e+01
  angle pdb=" CB  HIS A 262 "
        pdb=" CG  HIS A 262 "
        pdb=" CD2 HIS A 262 "
      ideal   model   delta    sigma   weight residual
     131.20  125.07    6.13 1.30e+00 5.92e-01 2.22e+01
  angle pdb=" CA  PHE A 211 "
        pdb=" CB  PHE A 211 "
        pdb=" CG  PHE A 211 "
      ideal   model   delta    sigma   weight residual
     113.80  118.45   -4.65 1.00e+00 1.00e+00 2.16e+01
  ... (remaining 25506 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.22: 6159
       17.22 -    34.44: 406
       34.44 -    51.66: 105
       51.66 -    68.88: 109
       68.88 -    86.10: 9
  Dihedral angle restraints: 6788
    sinusoidal: 3630
      harmonic: 3158
  Sorted by residual:
  dihedral pdb=" C   ASN A 254 "
           pdb=" N   ASN A 254 "
           pdb=" CA  ASN A 254 "
           pdb=" CB  ASN A 254 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.79   15.19     0      2.50e+00 1.60e-01 3.69e+01
  dihedral pdb=" CA  ARG A 589 "
           pdb=" C   ARG A 589 "
           pdb=" N   THR A 590 "
           pdb=" CA  THR A 590 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.95   29.05     0      5.00e+00 4.00e-02 3.38e+01
  dihedral pdb=" CA  ASN A 254 "
           pdb=" C   ASN A 254 "
           pdb=" N   MET A 255 "
           pdb=" CA  MET A 255 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.85   25.15     0      5.00e+00 4.00e-02 2.53e+01
  ... (remaining 6785 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.108: 790
       0.108 -    0.216: 227
       0.216 -    0.325: 35
       0.325 -    0.433: 3
       0.433 -    0.541: 1
  Chirality restraints: 1056
  Sorted by residual:
  chirality pdb=" CA  ASN A 254 "
            pdb=" N   ASN A 254 "
            pdb=" C   ASN A 254 "
            pdb=" CB  ASN A 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.32e+00
  chirality pdb=" CA  ASN A 160 "
            pdb=" N   ASN A 160 "
            pdb=" C   ASN A 160 "
            pdb=" CB  ASN A 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.94e+00
  chirality pdb=" CA  ASP A  65 "
            pdb=" N   ASP A  65 "
            pdb=" C   ASP A  65 "
            pdb=" CB  ASP A  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.44e+00
  ... (remaining 1053 not shown)

  Planarity restraints: 2177
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 542 "    0.542 9.50e-02 1.11e+02   1.94e-01 1.49e+02
        pdb=" NE  ARG A 542 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 542 "   -0.031 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 542 "    0.015 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 542 "   -0.054 2.00e-02 2.50e+03
        pdb="HH11 ARG A 542 "    0.057 2.00e-02 2.50e+03
        pdb="HH12 ARG A 542 "   -0.113 2.00e-02 2.50e+03
        pdb="HH21 ARG A 542 "   -0.046 2.00e-02 2.50e+03
        pdb="HH22 ARG A 542 "    0.155 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 480 "   -0.039 9.50e-02 1.11e+02   7.76e-02 1.32e+02
        pdb=" NE  ARG A 480 "   -0.052 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 480 "   -0.064 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 480 "   -0.035 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 480 "   -0.087 2.00e-02 2.50e+03
        pdb="HH11 ARG A 480 "    0.129 2.00e-02 2.50e+03
        pdb="HH12 ARG A 480 "   -0.033 2.00e-02 2.50e+03
        pdb="HH21 ARG A 480 "    0.139 2.00e-02 2.50e+03
        pdb="HH22 ARG A 480 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  81 "   -0.405 9.50e-02 1.11e+02   1.52e-01 1.25e+02
        pdb=" NE  ARG A  81 "   -0.092 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  81 "    0.014 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  81 "    0.064 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  81 "    0.050 2.00e-02 2.50e+03
        pdb="HH11 ARG A  81 "    0.048 2.00e-02 2.50e+03
        pdb="HH12 ARG A  81 "   -0.036 2.00e-02 2.50e+03
        pdb="HH21 ARG A  81 "    0.093 2.00e-02 2.50e+03
        pdb="HH22 ARG A  81 "   -0.124 2.00e-02 2.50e+03
  ... (remaining 2174 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.20: 1111
        2.20 -     2.80: 24117
        2.80 -     3.40: 37588
        3.40 -     4.00: 52075
        4.00 -     4.60: 74942
  Nonbonded interactions: 189833
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 336 "
            pdb=" HG  SER A 338 "
     model   vdw
     1.595 2.450
  nonbonded pdb=" HG  SER A 660 "
            pdb=" OE1 GLU A 662 "
     model   vdw
     1.606 2.450
  nonbonded pdb=" OE2 GLU A 643 "
            pdb=" HH  TYR A 780 "
     model   vdw
     1.607 2.450
  nonbonded pdb=" OD1 ASP A  26 "
            pdb=" HG  SER A  29 "
     model   vdw
     1.608 2.450
  nonbonded pdb=" OD1 ASP A 395 "
            pdb=" HH  TYR A 411 "
     model   vdw
     1.618 2.450
  ... (remaining 189828 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.060
  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:             0.110
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.430
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.043   7391  Z= 0.725
  Angle     :  1.791   7.764  10043  Z= 1.207
  Chirality :  0.098   0.541   1056
  Planarity :  0.015   0.207   1325
  Dihedral  : 13.127  86.103   2709
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 0.36
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  2.49 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  2.94 %
    Favored  : 96.03 %
  Cbeta Deviations :  0.72 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.27), residues: 884
  helix: -0.90 (0.43), residues: 97
  sheet:  1.22 (0.25), residues: 398
  loop : -0.85 (0.29), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 542 
 TYR   0.092   0.017   TYR A 704 
 PHE   0.051   0.011   PHE A 377 
 TRP   0.083   0.016   TRP A 272 
 HIS   0.015   0.004   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.01228 ( 7389)
  covalent geometry    : angle       1.79100 (10039)
  SS BOND              : bond        0.02469 (    2)
  SS BOND              : angle       2.64425 (    4)
  hydrogen bonds       : bond        0.12884 (  376)
  hydrogen bonds       : angle       7.72264 ( 1125)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 187
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 MET cc_start: 0.7165 (mmm) cc_final: 0.6426 (mmp)
REVERT: A  125 TRP cc_start: 0.4610 (t60) cc_final: 0.4226 (t60)
REVERT: A  148 ARG cc_start: 0.6966 (ptt90) cc_final: 0.6745 (ptt180)
REVERT: A  164 ILE cc_start: 0.5534 (tt) cc_final: 0.5235 (tp)
REVERT: A  166 ASP cc_start: 0.6798 (m-30) cc_final: 0.6476 (m-30)
REVERT: A  182 VAL cc_start: 0.7310 (OUTLIER) cc_final: 0.6921 (p)
REVERT: A  277 ARG cc_start: 0.6995 (mtp180) cc_final: 0.6316 (tmt170)
REVERT: A  321 MET cc_start: 0.8006 (ttp) cc_final: 0.7776 (ttp)
REVERT: A  332 THR cc_start: 0.8166 (t) cc_final: 0.7928 (m)
REVERT: A  346 LYS cc_start: 0.7689 (mttt) cc_final: 0.7469 (mtpt)
REVERT: A  421 ARG cc_start: 0.6682 (mtp85) cc_final: 0.6394 (mtp180)
REVERT: A  475 ASP cc_start: 0.7807 (m-30) cc_final: 0.7210 (t70)
REVERT: A  476 GLU cc_start: 0.7406 (tt0) cc_final: 0.7110 (mm-30)
REVERT: A  477 SER cc_start: 0.8197 (t) cc_final: 0.7990 (t)
REVERT: A  496 ASP cc_start: 0.7757 (m-30) cc_final: 0.7462 (t0)
REVERT: A  559 THR cc_start: 0.8216 (t) cc_final: 0.7716 (t)
REVERT: B   76 ARG cc_start: 0.7654 (ttt180) cc_final: 0.7158 (tmm160)
REVERT: B   91 ARG cc_start: 0.8110 (mtp180) cc_final: 0.7902 (mmp80)
REVERT: B  109 LEU cc_start: 0.7216 (mp) cc_final: 0.6752 (tt)
REVERT: B  153 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7724 (mt-10)
  outliers start: 8
  outliers final: 2
  residues processed: 194
  average time/residue: 0.9521
  time to fit residues: 196.3553
Evaluate side-chains
  135 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 132
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  210 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
A 745 HIS
A 782 ASN
B  28 GLN
B  53 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.185170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.141750 restraints weight = 18507.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 1.56
r_work: 0.3538 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7391  Z= 0.150
  Angle     :  0.602   4.178  10043  Z= 0.337
  Chirality :  0.047   0.158   1056
  Planarity :  0.005   0.044   1325
  Dihedral  :  6.268  26.357   1008
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 1.64
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  2.94 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  9.09 %
    Favored  : 89.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.27), residues: 884
  helix:  0.90 (0.50), residues: 100
  sheet:  0.63 (0.25), residues: 399
  loop : -0.74 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 542 
 TYR   0.022   0.001   TYR A 347 
 PHE   0.013   0.001   PHE A 243 
 TRP   0.007   0.001   TRP A 272 
 HIS   0.004   0.001   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7389)
  covalent geometry    : angle       0.60170 (10039)
  SS BOND              : bond        0.00384 (    2)
  SS BOND              : angle       0.98826 (    4)
  hydrogen bonds       : bond        0.04478 (  376)
  hydrogen bonds       : angle       6.12259 ( 1125)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 138
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 ARG cc_start: 0.7219 (ptt90) cc_final: 0.7005 (ptt180)
REVERT: A  150 LYS cc_start: 0.6367 (mmtt) cc_final: 0.5802 (pttm)
REVERT: A  164 ILE cc_start: 0.5923 (tt) cc_final: 0.5723 (mp)
REVERT: A  182 VAL cc_start: 0.7444 (t) cc_final: 0.7062 (p)
REVERT: A  275 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6759 (tt0)
REVERT: A  277 ARG cc_start: 0.7046 (mtp180) cc_final: 0.6525 (mmt180)
REVERT: A  332 THR cc_start: 0.8237 (t) cc_final: 0.7905 (m)
REVERT: A  421 ARG cc_start: 0.6758 (mtp85) cc_final: 0.6515 (mtp180)
REVERT: A  475 ASP cc_start: 0.7884 (m-30) cc_final: 0.7396 (t70)
REVERT: A  476 GLU cc_start: 0.7441 (tt0) cc_final: 0.7176 (tt0)
REVERT: A  500 LEU cc_start: 0.6993 (tp) cc_final: 0.6687 (tp)
REVERT: A  618 GLU cc_start: 0.7161 (tt0) cc_final: 0.6570 (mp0)
REVERT: A  711 LYS cc_start: 0.8120 (mttt) cc_final: 0.7666 (mttm)
REVERT: A  712 GLN cc_start: 0.8087 (pt0) cc_final: 0.7660 (pt0)
REVERT: B   76 ARG cc_start: 0.7293 (ttt180) cc_final: 0.6385 (tmm160)
REVERT: B   79 LYS cc_start: 0.8046 (tttt) cc_final: 0.7470 (ttpt)
REVERT: B   91 ARG cc_start: 0.7917 (mtp180) cc_final: 0.7678 (mtm180)
REVERT: B  109 LEU cc_start: 0.6575 (mp) cc_final: 0.6016 (tt)
  outliers start: 13
  outliers final: 3
  residues processed: 143
  average time/residue: 1.1117
  time to fit residues: 168.1919
Evaluate side-chains
  124 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 121
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain B residue   81 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
A 167 ASN
A 232 ASN
A 254 ASN
A 755 ASN
A 770 GLN
B  53 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.180016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.136101 restraints weight = 18679.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 1.57
r_work: 0.3491 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.3493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7391  Z= 0.160
  Angle     :  0.572   3.911  10043  Z= 0.316
  Chirality :  0.047   0.161   1056
  Planarity :  0.005   0.052   1325
  Dihedral  :  5.686  22.470   1004
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  2.60 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 11.78 %
    Favored  : 86.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.28), residues: 884
  helix:  1.34 (0.54), residues: 93
  sheet:  0.41 (0.24), residues: 428
  loop : -0.73 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 574 
 TYR   0.015   0.002   TYR A 347 
 PHE   0.018   0.002   PHE A 243 
 TRP   0.009   0.001   TRP A 180 
 HIS   0.003   0.001   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 7389)
  covalent geometry    : angle       0.57196 (10039)
  SS BOND              : bond        0.00335 (    2)
  SS BOND              : angle       0.72600 (    4)
  hydrogen bonds       : bond        0.03968 (  376)
  hydrogen bonds       : angle       5.60909 ( 1125)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.6160 (mpp)
REVERT: A  150 LYS cc_start: 0.6391 (mmtt) cc_final: 0.5739 (pttm)
REVERT: A  182 VAL cc_start: 0.7354 (t) cc_final: 0.6930 (p)
REVERT: A  244 TYR cc_start: 0.6368 (OUTLIER) cc_final: 0.4845 (m-80)
REVERT: A  275 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6730 (tt0)
REVERT: A  277 ARG cc_start: 0.7021 (mtp180) cc_final: 0.6426 (mmt180)
REVERT: A  421 ARG cc_start: 0.6657 (mtp85) cc_final: 0.6312 (mtp180)
REVERT: A  475 ASP cc_start: 0.8138 (m-30) cc_final: 0.7671 (t70)
REVERT: A  476 GLU cc_start: 0.7658 (tt0) cc_final: 0.7281 (tp30)
REVERT: A  477 SER cc_start: 0.8440 (OUTLIER) cc_final: 0.7989 (m)
REVERT: A  499 MET cc_start: 0.5781 (ppp) cc_final: 0.5502 (ppp)
REVERT: A  615 ARG cc_start: 0.7343 (ttt180) cc_final: 0.6551 (tpt-90)
REVERT: A  618 GLU cc_start: 0.7081 (tt0) cc_final: 0.6422 (mp0)
REVERT: A  711 LYS cc_start: 0.8010 (mttt) cc_final: 0.7466 (mttm)
REVERT: B   76 ARG cc_start: 0.7202 (ttt180) cc_final: 0.6232 (tmm160)
REVERT: B   79 LYS cc_start: 0.8052 (tttt) cc_final: 0.7385 (ttpt)
REVERT: B   91 ARG cc_start: 0.7848 (mtp180) cc_final: 0.7094 (mmp80)
REVERT: B  109 LEU cc_start: 0.6553 (mp) cc_final: 0.5950 (tt)
  outliers start: 15
  outliers final: 4
  residues processed: 129
  average time/residue: 1.2076
  time to fit residues: 164.6451
Evaluate side-chains
  123 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  477 SER
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain B residue   81 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 63 optimal weight:    0.5980
   chunk 4 optimal weight:    0.4980
   chunk 66 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
B  28 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.181132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.137844 restraints weight = 19024.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 1.56
r_work: 0.3511 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3398 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.3827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7391  Z= 0.113
  Angle     :  0.508   3.882  10043  Z= 0.279
  Chirality :  0.046   0.157   1056
  Planarity :  0.004   0.052   1325
  Dihedral  :  5.228  20.709   1004
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  2.60 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.42 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.29), residues: 884
  helix:  1.57 (0.55), residues: 93
  sheet:  0.44 (0.25), residues: 419
  loop : -0.62 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 469 
 TYR   0.011   0.001   TYR A 347 
 PHE   0.013   0.001   PHE A 243 
 TRP   0.006   0.001   TRP A 199 
 HIS   0.003   0.001   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 7389)
  covalent geometry    : angle       0.50844 (10039)
  SS BOND              : bond        0.00309 (    2)
  SS BOND              : angle       0.54659 (    4)
  hydrogen bonds       : bond        0.03449 (  376)
  hydrogen bonds       : angle       5.31419 ( 1125)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 LYS cc_start: 0.6312 (mmtt) cc_final: 0.5690 (pttm)
REVERT: A  182 VAL cc_start: 0.7331 (t) cc_final: 0.6901 (p)
REVERT: A  198 ILE cc_start: 0.6601 (OUTLIER) cc_final: 0.6281 (mt)
REVERT: A  232 ASN cc_start: 0.6163 (OUTLIER) cc_final: 0.5298 (m-40)
REVERT: A  244 TYR cc_start: 0.6269 (OUTLIER) cc_final: 0.4714 (m-80)
REVERT: A  275 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6020 (tt0)
REVERT: A  277 ARG cc_start: 0.6985 (mtp180) cc_final: 0.6410 (mmt180)
REVERT: A  330 ASP cc_start: 0.8299 (t0) cc_final: 0.8059 (t0)
REVERT: A  346 LYS cc_start: 0.8265 (mtpt) cc_final: 0.7615 (mttm)
REVERT: A  421 ARG cc_start: 0.6604 (mtp85) cc_final: 0.6285 (mtp180)
REVERT: A  469 ARG cc_start: 0.6830 (mtp85) cc_final: 0.6531 (mtt-85)
REVERT: A  475 ASP cc_start: 0.8187 (m-30) cc_final: 0.7723 (t70)
REVERT: A  476 GLU cc_start: 0.7701 (tt0) cc_final: 0.7292 (tp30)
REVERT: A  477 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.7971 (m)
REVERT: A  615 ARG cc_start: 0.7300 (ttt180) cc_final: 0.6463 (tpt-90)
REVERT: A  618 GLU cc_start: 0.7128 (tt0) cc_final: 0.6487 (mp0)
REVERT: A  711 LYS cc_start: 0.7971 (mttt) cc_final: 0.7419 (mttm)
REVERT: A  733 GLU cc_start: 0.7771 (tp30) cc_final: 0.7338 (tp30)
REVERT: B   76 ARG cc_start: 0.7129 (ttt180) cc_final: 0.6166 (tmm160)
REVERT: B   79 LYS cc_start: 0.8025 (tttt) cc_final: 0.7347 (ttpt)
REVERT: B   91 ARG cc_start: 0.7828 (mtp180) cc_final: 0.7040 (mmp80)
REVERT: B  109 LEU cc_start: 0.6527 (mp) cc_final: 0.5910 (tt)
  outliers start: 18
  outliers final: 7
  residues processed: 129
  average time/residue: 1.0615
  time to fit residues: 145.3407
Evaluate side-chains
  128 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  477 SER
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue  107 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 43 optimal weight:    0.0170
   chunk 26 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0770
   chunk 71 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 72 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
A 167 ASN
A 232 ASN
A 269 ASN
A 345 ASN
A 770 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.182724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.142054 restraints weight = 19672.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 1.66
r_work: 0.3601 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3499 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.4039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7391  Z= 0.113
  Angle     :  0.497   3.958  10043  Z= 0.271
  Chirality :  0.045   0.163   1056
  Planarity :  0.004   0.053   1325
  Dihedral  :  5.010  19.299   1004
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  2.71 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 13.70 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.29), residues: 884
  helix:  1.73 (0.55), residues: 93
  sheet:  0.32 (0.25), residues: 430
  loop : -0.61 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 469 
 TYR   0.011   0.001   TYR A 537 
 PHE   0.016   0.001   PHE A 243 
 TRP   0.004   0.001   TRP A 180 
 HIS   0.003   0.001   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 7389)
  covalent geometry    : angle       0.49714 (10039)
  SS BOND              : bond        0.00321 (    2)
  SS BOND              : angle       0.54121 (    4)
  hydrogen bonds       : bond        0.03305 (  376)
  hydrogen bonds       : angle       5.18994 ( 1125)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.5879 (mpp)
REVERT: A  150 LYS cc_start: 0.6396 (mmtt) cc_final: 0.5780 (pttm)
REVERT: A  182 VAL cc_start: 0.7478 (t) cc_final: 0.7044 (p)
REVERT: A  244 TYR cc_start: 0.6383 (OUTLIER) cc_final: 0.4890 (m-80)
REVERT: A  275 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6327 (tm-30)
REVERT: A  277 ARG cc_start: 0.7101 (mtp180) cc_final: 0.6452 (mmt180)
REVERT: A  346 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7639 (mttm)
REVERT: A  347 TYR cc_start: 0.7332 (m-80) cc_final: 0.7072 (m-80)
REVERT: A  421 ARG cc_start: 0.6761 (mtp85) cc_final: 0.6428 (mtp180)
REVERT: A  469 ARG cc_start: 0.6945 (mtp85) cc_final: 0.6672 (mtt-85)
REVERT: A  475 ASP cc_start: 0.8261 (m-30) cc_final: 0.7781 (t70)
REVERT: A  476 GLU cc_start: 0.7810 (tt0) cc_final: 0.7457 (tp30)
REVERT: A  477 SER cc_start: 0.8458 (OUTLIER) cc_final: 0.8037 (m)
REVERT: A  615 ARG cc_start: 0.7389 (ttt180) cc_final: 0.6627 (tpt-90)
REVERT: A  618 GLU cc_start: 0.7195 (tt0) cc_final: 0.6544 (mp0)
REVERT: A  711 LYS cc_start: 0.8022 (mttt) cc_final: 0.7495 (mttm)
REVERT: A  733 GLU cc_start: 0.7814 (tp30) cc_final: 0.7467 (tp30)
REVERT: B   76 ARG cc_start: 0.7219 (ttt180) cc_final: 0.6297 (tmm160)
REVERT: B   79 LYS cc_start: 0.8009 (tttt) cc_final: 0.7327 (ttpt)
REVERT: B   91 ARG cc_start: 0.7849 (mtp180) cc_final: 0.7151 (mmp80)
REVERT: B  109 LEU cc_start: 0.6610 (mp) cc_final: 0.6010 (tt)
  outliers start: 17
  outliers final: 6
  residues processed: 122
  average time/residue: 1.0956
  time to fit residues: 141.8829
Evaluate side-chains
  121 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  456 THR
Chi-restraints excluded: chain A residue  477 SER
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue  107 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 39 optimal weight:    0.4980
   chunk 64 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
B  28 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.182332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.141761 restraints weight = 19652.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 1.65
r_work: 0.3599 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3500 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.4152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7391  Z= 0.116
  Angle     :  0.493   3.802  10043  Z= 0.269
  Chirality :  0.045   0.158   1056
  Planarity :  0.004   0.052   1325
  Dihedral  :  4.937  19.444   1004
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  2.83 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.34 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.29), residues: 884
  helix:  1.88 (0.55), residues: 93
  sheet:  0.32 (0.25), residues: 428
  loop : -0.55 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 469 
 TYR   0.011   0.001   TYR A 537 
 PHE   0.011   0.001   PHE A 243 
 TRP   0.004   0.001   TRP A 311 
 HIS   0.002   0.001   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 7389)
  covalent geometry    : angle       0.49302 (10039)
  SS BOND              : bond        0.00312 (    2)
  SS BOND              : angle       0.55396 (    4)
  hydrogen bonds       : bond        0.03281 (  376)
  hydrogen bonds       : angle       5.10060 ( 1125)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.5885 (mpp)
REVERT: A  150 LYS cc_start: 0.6400 (mmtt) cc_final: 0.5796 (pttm)
REVERT: A  182 VAL cc_start: 0.7474 (t) cc_final: 0.7047 (p)
REVERT: A  244 TYR cc_start: 0.6415 (OUTLIER) cc_final: 0.4911 (m-80)
REVERT: A  275 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6346 (tm-30)
REVERT: A  277 ARG cc_start: 0.7168 (mtp180) cc_final: 0.6523 (mmt180)
REVERT: A  332 THR cc_start: 0.8107 (t) cc_final: 0.7753 (m)
REVERT: A  346 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7644 (mttm)
REVERT: A  347 TYR cc_start: 0.7437 (m-80) cc_final: 0.7190 (m-80)
REVERT: A  469 ARG cc_start: 0.6980 (mtp85) cc_final: 0.6703 (mtt-85)
REVERT: A  475 ASP cc_start: 0.8265 (m-30) cc_final: 0.7763 (t0)
REVERT: A  476 GLU cc_start: 0.7876 (tt0) cc_final: 0.7522 (tp30)
REVERT: A  477 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8064 (m)
REVERT: A  578 SER cc_start: 0.8688 (OUTLIER) cc_final: 0.8453 (p)
REVERT: A  615 ARG cc_start: 0.7402 (ttt180) cc_final: 0.6641 (tpt-90)
REVERT: A  618 GLU cc_start: 0.7223 (tt0) cc_final: 0.6581 (mp0)
REVERT: A  711 LYS cc_start: 0.8052 (mttt) cc_final: 0.7530 (mttm)
REVERT: B   76 ARG cc_start: 0.7242 (ttt180) cc_final: 0.6330 (ttp80)
REVERT: B   79 LYS cc_start: 0.8024 (tttt) cc_final: 0.7357 (ttpt)
REVERT: B   91 ARG cc_start: 0.7852 (mtp180) cc_final: 0.7164 (mmp80)
REVERT: B  109 LEU cc_start: 0.6734 (mp) cc_final: 0.6110 (tt)
  outliers start: 18
  outliers final: 6
  residues processed: 123
  average time/residue: 1.0803
  time to fit residues: 140.9292
Evaluate side-chains
  123 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  456 THR
Chi-restraints excluded: chain A residue  477 SER
Chi-restraints excluded: chain A residue  578 SER
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue  107 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 46 optimal weight:    0.5980
   chunk 66 optimal weight:    0.2980
   chunk 83 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
A 167 ASN
A 232 ASN
A 269 ASN
A 770 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.182964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.142464 restraints weight = 19442.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3700 rms_B_bonded: 1.67
r_work: 0.3609 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3507 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.4274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7391  Z= 0.105
  Angle     :  0.484   4.758  10043  Z= 0.262
  Chirality :  0.045   0.157   1056
  Planarity :  0.004   0.051   1325
  Dihedral  :  4.797  18.783   1004
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.05 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.72 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.29), residues: 884
  helix:  2.05 (0.55), residues: 93
  sheet:  0.25 (0.24), residues: 464
  loop : -0.50 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 469 
 TYR   0.010   0.001   TYR A 537 
 PHE   0.016   0.001   PHE A 243 
 TRP   0.004   0.001   TRP A 311 
 HIS   0.003   0.001   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 7389)
  covalent geometry    : angle       0.48372 (10039)
  SS BOND              : bond        0.00283 (    2)
  SS BOND              : angle       0.52915 (    4)
  hydrogen bonds       : bond        0.03150 (  376)
  hydrogen bonds       : angle       5.01767 ( 1125)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.5877 (mpp)
REVERT: A  150 LYS cc_start: 0.6360 (mmtt) cc_final: 0.5793 (pttm)
REVERT: A  167 ASN cc_start: 0.6833 (t0) cc_final: 0.6371 (t0)
REVERT: A  182 VAL cc_start: 0.7457 (OUTLIER) cc_final: 0.7045 (p)
REVERT: A  232 ASN cc_start: 0.6422 (t0) cc_final: 0.5218 (m-40)
REVERT: A  244 TYR cc_start: 0.6349 (OUTLIER) cc_final: 0.4852 (m-80)
REVERT: A  275 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6276 (tm-30)
REVERT: A  277 ARG cc_start: 0.7146 (mtp180) cc_final: 0.6519 (mmt180)
REVERT: A  346 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7647 (mttm)
REVERT: A  347 TYR cc_start: 0.7412 (m-80) cc_final: 0.7181 (m-80)
REVERT: A  469 ARG cc_start: 0.6982 (mtp85) cc_final: 0.6717 (mtt-85)
REVERT: A  475 ASP cc_start: 0.8250 (m-30) cc_final: 0.7738 (t0)
REVERT: A  476 GLU cc_start: 0.7876 (tt0) cc_final: 0.7507 (tp30)
REVERT: A  477 SER cc_start: 0.8489 (OUTLIER) cc_final: 0.8066 (m)
REVERT: A  578 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.8468 (p)
REVERT: A  615 ARG cc_start: 0.7410 (ttt180) cc_final: 0.6623 (tpt-90)
REVERT: A  618 GLU cc_start: 0.7220 (tt0) cc_final: 0.6565 (mp0)
REVERT: A  711 LYS cc_start: 0.8042 (mttt) cc_final: 0.7519 (mttm)
REVERT: A  733 GLU cc_start: 0.7769 (tp30) cc_final: 0.7386 (tp30)
REVERT: B   76 ARG cc_start: 0.7280 (ttt180) cc_final: 0.6322 (ttp80)
REVERT: B   79 LYS cc_start: 0.8004 (tttt) cc_final: 0.7343 (ttpt)
REVERT: B   91 ARG cc_start: 0.7828 (mtp180) cc_final: 0.7145 (mmp80)
REVERT: B  109 LEU cc_start: 0.6682 (mp) cc_final: 0.6028 (tt)
  outliers start: 18
  outliers final: 8
  residues processed: 124
  average time/residue: 1.0787
  time to fit residues: 141.8961
Evaluate side-chains
  126 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  456 THR
Chi-restraints excluded: chain A residue  477 SER
Chi-restraints excluded: chain A residue  578 SER
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain B residue  107 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
A 269 ASN
A 755 ASN
B  28 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.178283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.137489 restraints weight = 19647.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 1.67
r_work: 0.3552 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3450 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.4346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7391  Z= 0.199
  Angle     :  0.567   4.346  10043  Z= 0.311
  Chirality :  0.048   0.162   1056
  Planarity :  0.005   0.055   1325
  Dihedral  :  5.317  23.344   1004
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.28 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 14.21 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.28), residues: 884
  helix:  1.67 (0.54), residues: 93
  sheet:  0.29 (0.25), residues: 426
  loop : -0.66 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 469 
 TYR   0.015   0.002   TYR A 537 
 PHE   0.011   0.002   PHE A 243 
 TRP   0.009   0.001   TRP A 249 
 HIS   0.004   0.001   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 7389)
  covalent geometry    : angle       0.56678 (10039)
  SS BOND              : bond        0.00463 (    2)
  SS BOND              : angle       0.75478 (    4)
  hydrogen bonds       : bond        0.03865 (  376)
  hydrogen bonds       : angle       5.33219 ( 1125)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 LYS cc_start: 0.6565 (mmtt) cc_final: 0.6027 (pttm)
REVERT: A  182 VAL cc_start: 0.7504 (OUTLIER) cc_final: 0.7114 (p)
REVERT: A  244 TYR cc_start: 0.6469 (OUTLIER) cc_final: 0.5074 (m-80)
REVERT: A  275 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6170 (tt0)
REVERT: A  277 ARG cc_start: 0.7183 (mtp180) cc_final: 0.6566 (tmt170)
REVERT: A  288 GLU cc_start: 0.7637 (tp30) cc_final: 0.7343 (mm-30)
REVERT: A  346 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7610 (mttm)
REVERT: A  347 TYR cc_start: 0.7598 (m-80) cc_final: 0.7313 (m-80)
REVERT: A  443 ASN cc_start: 0.7601 (m-40) cc_final: 0.7259 (m-40)
REVERT: A  459 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7773 (tm-30)
REVERT: A  469 ARG cc_start: 0.7022 (mtp85) cc_final: 0.6769 (mtt-85)
REVERT: A  475 ASP cc_start: 0.8350 (m-30) cc_final: 0.7820 (t70)
REVERT: A  476 GLU cc_start: 0.7922 (tt0) cc_final: 0.7606 (mm-30)
REVERT: A  615 ARG cc_start: 0.7509 (ttt180) cc_final: 0.6759 (tpt-90)
REVERT: A  618 GLU cc_start: 0.7227 (tt0) cc_final: 0.6555 (mp0)
REVERT: A  670 LYS cc_start: 0.7298 (tttt) cc_final: 0.6691 (mptp)
REVERT: A  711 LYS cc_start: 0.8082 (mttt) cc_final: 0.7581 (mttm)
REVERT: A  733 GLU cc_start: 0.7983 (tp30) cc_final: 0.7596 (tp30)
REVERT: B   76 ARG cc_start: 0.7364 (ttt180) cc_final: 0.6397 (ttp80)
REVERT: B   79 LYS cc_start: 0.8212 (tttt) cc_final: 0.7455 (ttpt)
REVERT: B   91 ARG cc_start: 0.7940 (mtp180) cc_final: 0.7201 (mmp80)
REVERT: B  109 LEU cc_start: 0.6751 (mp) cc_final: 0.6113 (tt)
  outliers start: 21
  outliers final: 10
  residues processed: 122
  average time/residue: 1.1018
  time to fit residues: 142.3120
Evaluate side-chains
  123 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  456 THR
Chi-restraints excluded: chain A residue  459 GLN
Chi-restraints excluded: chain A residue  477 SER
Chi-restraints excluded: chain A residue  578 SER
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue  107 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 75 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
A 146 GLN
A 167 ASN
A 232 ASN
A 269 ASN
A 367 ASN
A 755 ASN
B  28 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.178114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.137625 restraints weight = 19737.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 1.66
r_work: 0.3552 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3451 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.4475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7391  Z= 0.182
  Angle     :  0.550   4.535  10043  Z= 0.301
  Chirality :  0.047   0.162   1056
  Planarity :  0.006   0.101   1325
  Dihedral  :  5.326  22.848   1004
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.62 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.98 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.28), residues: 884
  helix:  1.64 (0.55), residues: 93
  sheet:  0.24 (0.25), residues: 426
  loop : -0.72 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 421 
 TYR   0.015   0.002   TYR A 537 
 PHE   0.014   0.001   PHE A 243 
 TRP   0.008   0.001   TRP A 249 
 HIS   0.003   0.001   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 7389)
  covalent geometry    : angle       0.55028 (10039)
  SS BOND              : bond        0.00358 (    2)
  SS BOND              : angle       0.77804 (    4)
  hydrogen bonds       : bond        0.03730 (  376)
  hydrogen bonds       : angle       5.32072 ( 1125)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 LYS cc_start: 0.6544 (mmtt) cc_final: 0.5931 (pttm)
REVERT: A  167 ASN cc_start: 0.6939 (t0) cc_final: 0.6478 (t0)
REVERT: A  182 VAL cc_start: 0.7457 (OUTLIER) cc_final: 0.7065 (p)
REVERT: A  244 TYR cc_start: 0.6472 (OUTLIER) cc_final: 0.5055 (m-80)
REVERT: A  275 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6641 (tt0)
REVERT: A  277 ARG cc_start: 0.7197 (mtp180) cc_final: 0.6573 (mtp85)
REVERT: A  288 GLU cc_start: 0.7658 (tp30) cc_final: 0.7343 (mm-30)
REVERT: A  346 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7637 (mttm)
REVERT: A  347 TYR cc_start: 0.7612 (m-80) cc_final: 0.7332 (m-80)
REVERT: A  443 ASN cc_start: 0.7614 (m-40) cc_final: 0.7286 (m-40)
REVERT: A  459 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7799 (tm-30)
REVERT: A  469 ARG cc_start: 0.6995 (mtp85) cc_final: 0.6740 (mtt-85)
REVERT: A  475 ASP cc_start: 0.8367 (m-30) cc_final: 0.7838 (t70)
REVERT: A  476 GLU cc_start: 0.7951 (tt0) cc_final: 0.7604 (mm-30)
REVERT: A  615 ARG cc_start: 0.7519 (ttt180) cc_final: 0.6731 (tpt-90)
REVERT: A  618 GLU cc_start: 0.7235 (tt0) cc_final: 0.6534 (mp0)
REVERT: A  670 LYS cc_start: 0.7267 (tttt) cc_final: 0.6682 (mptp)
REVERT: A  711 LYS cc_start: 0.8071 (mttt) cc_final: 0.7558 (mttm)
REVERT: A  733 GLU cc_start: 0.7939 (tp30) cc_final: 0.7604 (tp30)
REVERT: B   76 ARG cc_start: 0.7368 (ttt180) cc_final: 0.6396 (ttp80)
REVERT: B   79 LYS cc_start: 0.8223 (tttt) cc_final: 0.7509 (ttpt)
REVERT: B   91 ARG cc_start: 0.7937 (mtp180) cc_final: 0.7190 (mmp80)
REVERT: B  109 LEU cc_start: 0.6699 (mp) cc_final: 0.6071 (tt)
  outliers start: 17
  outliers final: 11
  residues processed: 119
  average time/residue: 1.0099
  time to fit residues: 127.9099
Evaluate side-chains
  122 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  456 THR
Chi-restraints excluded: chain A residue  459 GLN
Chi-restraints excluded: chain A residue  477 SER
Chi-restraints excluded: chain A residue  578 SER
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue  107 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 6 optimal weight:    9.9990
   chunk 82 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
A 232 ASN
B  28 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.179778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.139384 restraints weight = 19591.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 1.65
r_work: 0.3575 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.4517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7391  Z= 0.118
  Angle     :  0.514   4.304  10043  Z= 0.280
  Chirality :  0.046   0.161   1056
  Planarity :  0.005   0.072   1325
  Dihedral  :  5.094  21.423   1004
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.73 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.11 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.29), residues: 884
  helix:  1.87 (0.55), residues: 93
  sheet:  0.19 (0.25), residues: 427
  loop : -0.64 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 421 
 TYR   0.012   0.001   TYR A 537 
 PHE   0.013   0.001   PHE A 243 
 TRP   0.005   0.001   TRP A 249 
 HIS   0.002   0.001   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 7389)
  covalent geometry    : angle       0.51406 (10039)
  SS BOND              : bond        0.00334 (    2)
  SS BOND              : angle       0.56835 (    4)
  hydrogen bonds       : bond        0.03405 (  376)
  hydrogen bonds       : angle       5.21267 ( 1125)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 LYS cc_start: 0.6458 (mmtt) cc_final: 0.5853 (pttm)
REVERT: A  182 VAL cc_start: 0.7458 (OUTLIER) cc_final: 0.7065 (p)
REVERT: A  235 TYR cc_start: 0.6445 (t80) cc_final: 0.6179 (t80)
REVERT: A  244 TYR cc_start: 0.6307 (OUTLIER) cc_final: 0.4903 (m-80)
REVERT: A  275 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6661 (tp30)
REVERT: A  277 ARG cc_start: 0.7187 (mtp180) cc_final: 0.6565 (mtp85)
REVERT: A  288 GLU cc_start: 0.7643 (tp30) cc_final: 0.7352 (mm-30)
REVERT: A  346 LYS cc_start: 0.8229 (mtpt) cc_final: 0.7626 (mttm)
REVERT: A  347 TYR cc_start: 0.7587 (m-80) cc_final: 0.7349 (m-80)
REVERT: A  459 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7755 (tm-30)
REVERT: A  469 ARG cc_start: 0.6996 (mtp85) cc_final: 0.6737 (mtt-85)
REVERT: A  475 ASP cc_start: 0.8329 (m-30) cc_final: 0.7801 (t70)
REVERT: A  476 GLU cc_start: 0.7924 (tt0) cc_final: 0.7564 (mm-30)
REVERT: A  615 ARG cc_start: 0.7484 (ttt180) cc_final: 0.6692 (tpt-90)
REVERT: A  618 GLU cc_start: 0.7215 (tt0) cc_final: 0.6513 (mp0)
REVERT: A  670 LYS cc_start: 0.7218 (tttt) cc_final: 0.6626 (mptp)
REVERT: A  711 LYS cc_start: 0.8036 (mttt) cc_final: 0.7522 (mttm)
REVERT: A  733 GLU cc_start: 0.7878 (tp30) cc_final: 0.7563 (tp30)
REVERT: B   76 ARG cc_start: 0.7318 (ttt180) cc_final: 0.6353 (ttp80)
REVERT: B   79 LYS cc_start: 0.8207 (tttt) cc_final: 0.7491 (ttpt)
REVERT: B   91 ARG cc_start: 0.7890 (mtp180) cc_final: 0.7131 (mmp80)
REVERT: B  109 LEU cc_start: 0.6661 (mp) cc_final: 0.6023 (tt)
  outliers start: 14
  outliers final: 9
  residues processed: 121
  average time/residue: 1.0688
  time to fit residues: 137.1813
Evaluate side-chains
  121 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  456 THR
Chi-restraints excluded: chain A residue  459 GLN
Chi-restraints excluded: chain A residue  477 SER
Chi-restraints excluded: chain A residue  578 SER
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain B residue  107 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 75 optimal weight:    0.4980
   chunk 64 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
A 167 ASN
A 443 ASN
B  28 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.180573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.140409 restraints weight = 19592.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 1.63
r_work: 0.3586 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3485 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.4628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7391  Z= 0.120
  Angle     :  0.502   3.891  10043  Z= 0.273
  Chirality :  0.045   0.158   1056
  Planarity :  0.004   0.053   1325
  Dihedral  :  4.952  20.163   1004
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.85 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.62 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.29), residues: 884
  helix:  2.02 (0.56), residues: 93
  sheet:  0.28 (0.25), residues: 419
  loop : -0.66 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 469 
 TYR   0.012   0.001   TYR A 537 
 PHE   0.014   0.001   PHE A 243 
 TRP   0.005   0.001   TRP A 199 
 HIS   0.002   0.001   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7389)
  covalent geometry    : angle       0.50235 (10039)
  SS BOND              : bond        0.00322 (    2)
  SS BOND              : angle       0.62193 (    4)
  hydrogen bonds       : bond        0.03302 (  376)
  hydrogen bonds       : angle       5.10351 ( 1125)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5522.81 seconds
wall clock time: 94 minutes 1.03 seconds (5641.03 seconds total)