Starting phenix.real_space_refine
on Fri Feb 14 07:57:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j1j_35926/02_2025/8j1j_35926.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j1j_35926/02_2025/8j1j_35926.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j1j_35926/02_2025/8j1j_35926.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j1j_35926/02_2025/8j1j_35926.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j1j_35926/02_2025/8j1j_35926.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j1j_35926/02_2025/8j1j_35926.cif"
  }
  resolution = 2.91
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.010 sd=   0.077
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: 7
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     151      5.49       5
     Mg      2      5.21       5
     S      34      5.16       5
     C    5613      2.51       5
     N    1771      2.21       5
     O    2220      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9793
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 424, 3437
          Classifications: {'peptide': 424}
          Link IDs: {'PTRANS': 10, 'TRANS': 413}
    Chain: "D"
      Number of atoms: 570
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 570
          Classifications: {'DNA': 28}
          Link IDs: {'rna3p': 27}
    Chain: "E"
      Number of atoms: 224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 224
          Classifications: {'DNA': 11}
          Link IDs: {'rna3p': 10}
    Chain: "C"
      Number of atoms: 2408
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 2408
          Classifications: {'RNA': 112}
          Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 1, 'rna3p_pur': 58, 'rna3p_pyr': 44}
          Link IDs: {'rna2p': 10, 'rna3p': 101}
    Chain: "B"
      Number of atoms: 3150
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 387, 3150
          Classifications: {'peptide': 387}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 377}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3063  SG  CYS A 372      89.022  57.120  33.002  1.00 89.59           S
  ATOM   3084  SG  CYS A 375      91.419  56.554  33.615  1.00 77.07           S
  ATOM   3201  SG  CYS A 391      90.464  58.956  36.815  1.00120.51           S
  ATOM   3223  SG  CYS A 394      91.781  58.761  32.523  1.00109.28           S
  ATOM   9461  SG  CYS B 372      62.724  88.689  63.390  1.00116.48           S
  ATOM   9482  SG  CYS B 375      65.516  90.455  66.073  1.00132.46           S
  ATOM   9562  SG  CYS B 391      65.774  89.756  62.345  1.00137.00           S
  ATOM   9584  SG  CYS B 394      65.199  87.078  63.799  1.00140.29           S

  Time building chain proxies: 6.44, per 1000 atoms: 0.66
  Number of scatterers: 9793
  At special positions: 0
  Unit cell: (103.584, 114.208, 112.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     S      34     16.00
     P     151     15.00
     Mg      2     11.99
     O    2220      8.00
     N    1771      7.00
     C    5613      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.40
  Conformation dependent library (CDL) restraints added in 910.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 375 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 394 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 372 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 391 "
      pdb="  ZN B 501 "
        pdb="ZN    ZN B 501 " - pdb=" SG  CYS B 375 "
        pdb="ZN    ZN B 501 " - pdb=" SG  CYS B 394 "
        pdb="ZN    ZN B 501 " - pdb=" SG  CYS B 391 "
        pdb="ZN    ZN B 501 " - pdb=" SG  CYS B 372 "
      Number of angles added : 12


  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1518

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      47.3% alpha, 15.8% beta
      55 base pairs and 101 stacking pairs defined.
    Time for finding SS restraints: 3.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 57
      removed outlier: 3.650A  pdb=" N   THR A  22 " --> pdb=" O   LYS A  18 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ARG A  32 " --> pdb=" O   GLN A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 66
    Processing helix  chain 'A' and resid 70 through 80
      removed outlier: 3.722A  pdb=" N   TYR A  74 " --> pdb=" O   ASN A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 105
      removed outlier: 3.516A  pdb=" N   ALA A  98 " --> pdb=" O   THR A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 111
    Processing helix  chain 'A' and resid 128 through 130
      No H-bonds generated for 'chain 'A' and resid 128 through 130'
    Processing helix  chain 'A' and resid 150 through 155
    Processing helix  chain 'A' and resid 171 through 181
      removed outlier: 3.713A  pdb=" N   THR A 175 " --> pdb=" O   GLY A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 268
      removed outlier: 4.060A  pdb=" N   ARG A 260 " --> pdb=" O   GLN A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 271
      No H-bonds generated for 'chain 'A' and resid 269 through 271'
    Processing helix  chain 'A' and resid 272 through 276
    Processing helix  chain 'A' and resid 278 through 284
      removed outlier: 3.961A  pdb=" N   LYS A 282 " --> pdb=" O   HIS A 278 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG A 283 " --> pdb=" O   GLY A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 291
      removed outlier: 3.951A  pdb=" N   GLN A 289 " --> pdb=" O   PRO A 286 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ARG A 291 " --> pdb=" O   GLU A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 316
    Processing helix  chain 'A' and resid 326 through 329
    Processing helix  chain 'A' and resid 341 through 355
      removed outlier: 3.643A  pdb=" N   GLU A 355 " --> pdb=" O   TYR A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 409
      removed outlier: 4.009A  pdb=" N   ILE A 408 " --> pdb=" O   ALA A 404 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA A 409 " --> pdb=" O   ALA A 405 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 404 through 409'
    Processing helix  chain 'A' and resid 412 through 419
      removed outlier: 3.731A  pdb=" N   ALA A 418 " --> pdb=" O   ASP A 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 46
    Processing helix  chain 'B' and resid 50 through 55
      removed outlier: 3.604A  pdb=" N   ASN B  55 " --> pdb=" O   TYR B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 81
      removed outlier: 4.239A  pdb=" N   THR B  81 " --> pdb=" O   HIS B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 105
    Processing helix  chain 'B' and resid 105 through 112
    Processing helix  chain 'B' and resid 150 through 158
      removed outlier: 3.533A  pdb=" N   GLU B 156 " --> pdb=" O   PRO B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 183
      removed outlier: 3.577A  pdb=" N   THR B 175 " --> pdb=" O   GLY B 171 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ARG B 179 " --> pdb=" O   THR B 175 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   SER B 182 " --> pdb=" O   ASP B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 264
    Processing helix  chain 'B' and resid 286 through 315
    Processing helix  chain 'B' and resid 341 through 354
      removed outlier: 4.054A  pdb=" N   TYR B 351 " --> pdb=" O   GLN B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 410
    Processing helix  chain 'B' and resid 412 through 421
      removed outlier: 3.641A  pdb=" N   ILE B 416 " --> pdb=" O   ASN B 412 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   SER B 420 " --> pdb=" O   ILE B 416 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5
    Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 5
    Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 12
      removed outlier: 6.692A  pdb=" N   ILE A 166 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   SER A 164 " --> pdb=" O   PRO A  12 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   TYR A 142 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 245
      removed outlier: 3.630A  pdb=" N   ALA A 232 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   GLU A 324 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 388 through 390
      removed outlier: 3.653A  pdb=" N   ALA A 398 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 3
      removed outlier: 6.748A  pdb=" N   ASN B 204 " --> pdb=" O   SER B 190 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   SER B 190 " --> pdb=" O   ASN B 204 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   SER B 206 " --> pdb=" O   HIS B 188 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 12
      removed outlier: 6.703A  pdb=" N   ILE B 166 " --> pdb=" O   VAL B  10 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   SER B 164 " --> pdb=" O   PRO B  12 " (cutoff:3.500A)
      removed outlier: 4.981A  pdb=" N   TYR B 142 " --> pdb=" O   ILE B 167 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASP B 141 " --> pdb=" O   MET B 137 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 194 through 195
    Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 245
      removed outlier: 8.784A  pdb=" N   CYS B 318 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   LYS B 220 " --> pdb=" O   CYS B 318 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR B 320 " --> pdb=" O   LYS B 220 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 388 through 390

    331 hydrogen bonds defined for protein.
    939 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      138 hydrogen bonds
      256 hydrogen bond angles
      0 basepair planarities
      55 basepair parallelities
      101 stacking parallelities
  Total time for adding SS restraints: 3.22

  Time building geometry restraints manager: 2.81 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2576
        1.33 -     1.46: 2782
        1.46 -     1.58: 4576
        1.58 -     1.70: 299
        1.70 -     1.82: 58
  Bond restraints: 10291
  Sorted by residual:
  bond pdb=" C   ARG B 170 "
       pdb=" N   GLY B 171 "
    ideal  model  delta    sigma   weight residual
    1.335  1.316  0.018 7.50e-03 1.78e+04 5.95e+00
  bond pdb=" C   LYS B 285 "
       pdb=" N   PRO B 286 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.023 1.30e-02 5.92e+03 3.18e+00
  bond pdb=" O4'  DT D  14 "
       pdb=" C1'  DT D  14 "
    ideal  model  delta    sigma   weight residual
    1.414  1.394  0.020 2.00e-02 2.50e+03 1.05e+00
  bond pdb=" N   TYR A 270 "
       pdb=" CA  TYR A 270 "
    ideal  model  delta    sigma   weight residual
    1.464  1.452  0.012 1.36e-02 5.41e+03 7.72e-01
  bond pdb=" CB  VAL A  10 "
       pdb=" CG2 VAL A  10 "
    ideal  model  delta    sigma   weight residual
    1.521  1.492  0.029 3.30e-02 9.18e+02 7.60e-01
  ... (remaining 10286 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 13761
        1.04 -     2.08: 687
        2.08 -     3.12: 110
        3.12 -     4.16: 23
        4.16 -     5.20: 5
  Bond angle restraints: 14586
  Sorted by residual:
  angle pdb=" N   ILE A 284 "
        pdb=" CA  ILE A 284 "
        pdb=" C   ILE A 284 "
      ideal   model   delta    sigma   weight residual
     112.29  107.22    5.07 9.40e-01 1.13e+00 2.91e+01
  angle pdb=" N   SER A   0 "
        pdb=" CA  SER A   0 "
        pdb=" CB  SER A   0 "
      ideal   model   delta    sigma   weight residual
     114.17  110.22    3.95 1.14e+00 7.69e-01 1.20e+01
  angle pdb=" N   GLU A 156 "
        pdb=" CA  GLU A 156 "
        pdb=" C   GLU A 156 "
      ideal   model   delta    sigma   weight residual
     113.43  109.32    4.11 1.26e+00 6.30e-01 1.06e+01
  angle pdb=" N   VAL A  71 "
        pdb=" CA  VAL A  71 "
        pdb=" C   VAL A  71 "
      ideal   model   delta    sigma   weight residual
     112.50  108.20    4.30 1.39e+00 5.18e-01 9.55e+00
  angle pdb=" N   LYS B 198 "
        pdb=" CA  LYS B 198 "
        pdb=" C   LYS B 198 "
      ideal   model   delta    sigma   weight residual
     114.39  110.30    4.09 1.45e+00 4.76e-01 7.94e+00
  ... (remaining 14581 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.72: 5205
       15.72 -    31.44: 567
       31.44 -    47.15: 232
       47.15 -    62.87: 163
       62.87 -    78.59: 87
  Dihedral angle restraints: 6254
    sinusoidal: 3881
      harmonic: 2373
  Sorted by residual:
  dihedral pdb=" CA  ARG A 392 "
           pdb=" C   ARG A 392 "
           pdb=" N   ALA A 393 "
           pdb=" CA  ALA A 393 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.41   24.59     0      5.00e+00 4.00e-02 2.42e+01
  dihedral pdb=" CA  ASN A 382 "
           pdb=" CB  ASN A 382 "
           pdb=" CG  ASN A 382 "
           pdb=" OD1 ASN A 382 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -172.29  -67.71     2      2.00e+01 2.50e-03 1.03e+01
  dihedral pdb=" CA  ASN A  87 "
           pdb=" CB  ASN A  87 "
           pdb=" CG  ASN A  87 "
           pdb=" OD1 ASN A  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -172.70  -67.30     2      2.00e+01 2.50e-03 1.02e+01
  ... (remaining 6251 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1194
       0.035 -    0.071: 379
       0.071 -    0.106: 80
       0.106 -    0.141: 23
       0.141 -    0.177: 3
  Chirality restraints: 1679
  Sorted by residual:
  chirality pdb=" C1'   G C -68 "
            pdb=" O4'   G C -68 "
            pdb=" C2'   G C -68 "
            pdb=" N9    G C -68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.28    0.18 2.00e-01 2.50e+01 7.79e-01
  chirality pdb=" C1'   G C -44 "
            pdb=" O4'   G C -44 "
            pdb=" C2'   G C -44 "
            pdb=" N9    G C -44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.29    0.17 2.00e-01 2.50e+01 6.94e-01
  chirality pdb=" C1'   A C -18 "
            pdb=" O4'   A C -18 "
            pdb=" C2'   A C -18 "
            pdb=" N9    A C -18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.31    0.15 2.00e-01 2.50e+01 5.74e-01
  ... (remaining 1676 not shown)

  Planarity restraints: 1310
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C -44 "   -0.034 2.00e-02 2.50e+03   1.49e-02 6.64e+00
        pdb=" N9    G C -44 "    0.037 2.00e-02 2.50e+03
        pdb=" C8    G C -44 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    G C -44 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    G C -44 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    G C -44 "   -0.002 2.00e-02 2.50e+03
        pdb=" O6    G C -44 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1    G C -44 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    G C -44 "    0.000 2.00e-02 2.50e+03
        pdb=" N2    G C -44 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G C -44 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    G C -44 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C -68 "   -0.028 2.00e-02 2.50e+03   1.18e-02 4.21e+00
        pdb=" N9    G C -68 "    0.028 2.00e-02 2.50e+03
        pdb=" C8    G C -68 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    G C -68 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G C -68 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G C -68 "   -0.005 2.00e-02 2.50e+03
        pdb=" O6    G C -68 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    G C -68 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G C -68 "    0.000 2.00e-02 2.50e+03
        pdb=" N2    G C -68 "    0.005 2.00e-02 2.50e+03
        pdb=" N3    G C -68 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    G C -68 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 123 "    0.029 5.00e-02 4.00e+02   4.37e-02 3.06e+00
        pdb=" N   PRO B 124 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO B 124 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 124 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1307 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1588
        2.76 -     3.30: 8613
        3.30 -     3.83: 17692
        3.83 -     4.37: 22088
        4.37 -     4.90: 32757
  Nonbonded interactions: 82738
  Sorted by model distance:
  nonbonded pdb=" OP1   U C -41 "
            pdb=" NZ  LYS B 103 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" O2'   A C -54 "
            pdb=" OG  SER B  92 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" NE2 GLN A  28 "
            pdb=" OD1 ASP A 122 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" NH1 ARG A 298 "
            pdb=" OP1  DA D  12 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" OG  SER A 150 "
            pdb=" OP1  DT E  -4 "
     model   vdw
     2.304 3.040
  ... (remaining 82733 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 58 or resid 65 through 224 or (resid 225 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 226 through 265 or re \ 
sid 285 through 326 or resid 331 through 379 or resid 385 through 421 or resid 5 \ 
01))
  selection = chain 'B'
}

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:             0.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     28.350
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
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      :  0.004   0.032  10291  Z= 0.235
  Angle     :  0.531   5.196  14586  Z= 0.324
  Chirality :  0.038   0.177   1679
  Planarity :  0.003   0.044   1310
  Dihedral  : 18.679  78.587   4736
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  2.88 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  6.71 %
    Favored  : 91.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.28), residues: 799
  helix: -0.19 (0.26), residues: 362
  sheet: -0.51 (0.42), residues: 151
  loop : -1.66 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  43 
 HIS   0.006   0.001   HIS A 238 
 PHE   0.009   0.002   PHE A 102 
 TYR   0.014   0.001   TYR A  52 
 ARG   0.002   0.000   ARG A 260 

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

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

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 225
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.8200 (mtp85) cc_final: 0.7892 (mpt90)
REVERT: A   61 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8128 (mptm)
REVERT: A   87 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8581 (t0)
REVERT: A  108 GLU cc_start: 0.8340 (mp0) cc_final: 0.8056 (mp0)
REVERT: A  129 LYS cc_start: 0.8605 (ttpt) cc_final: 0.8390 (ttpp)
REVERT: A  174 LYS cc_start: 0.8731 (tttt) cc_final: 0.8398 (tttm)
REVERT: A  178 ASP cc_start: 0.8808 (m-30) cc_final: 0.8531 (m-30)
REVERT: A  222 MET cc_start: 0.9140 (ttp) cc_final: 0.8881 (ttp)
REVERT: A  244 LYS cc_start: 0.8702 (pttt) cc_final: 0.8496 (pttt)
REVERT: A  264 MET cc_start: 0.8490 (mtt) cc_final: 0.8186 (mtm)
REVERT: A  312 MET cc_start: 0.8735 (mmp) cc_final: 0.7680 (mmt)
REVERT: A  325 ASP cc_start: 0.8452 (t0) cc_final: 0.8161 (t70)
REVERT: A  344 ASP cc_start: 0.8200 (t0) cc_final: 0.7899 (t70)
REVERT: A  377 ASN cc_start: 0.8300 (t0) cc_final: 0.7044 (p0)
REVERT: A  412 ASN cc_start: 0.8074 (m-40) cc_final: 0.7732 (p0)
REVERT: B   18 LYS cc_start: 0.8400 (tttt) cc_final: 0.8199 (tttt)
REVERT: B   26 GLN cc_start: 0.8543 (mt0) cc_final: 0.8170 (mt0)
REVERT: B   29 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8119 (mm-40)
REVERT: B   71 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8727 (p)
REVERT: B  177 MET cc_start: 0.8347 (tpp) cc_final: 0.7888 (tpp)
REVERT: B  199 ASN cc_start: 0.8373 (t0) cc_final: 0.8129 (t0)
REVERT: B  208 ASP cc_start: 0.7571 (t0) cc_final: 0.7267 (t0)
REVERT: B  222 MET cc_start: 0.8748 (ttp) cc_final: 0.8345 (ttt)
REVERT: B  242 ARG cc_start: 0.8415 (ptp-170) cc_final: 0.8174 (ptp-170)
REVERT: B  249 GLU cc_start: 0.8283 (pm20) cc_final: 0.8037 (pm20)
REVERT: B  263 SER cc_start: 0.8550 (m) cc_final: 0.8330 (t)
REVERT: B  306 SER cc_start: 0.8526 (m) cc_final: 0.8124 (p)
REVERT: B  316 MET cc_start: 0.8328 (mmm) cc_final: 0.8006 (mmm)
REVERT: B  339 ASN cc_start: 0.8424 (t0) cc_final: 0.8174 (t0)
REVERT: B  351 TYR cc_start: 0.7885 (t80) cc_final: 0.7674 (t80)
REVERT: B  364 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7159 (m-30)
  outliers start: 10
  outliers final: 2
  residues processed: 235
  average time/residue: 1.5707
  time to fit residues: 389.1173
Evaluate side-chains
  188 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 183
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  364 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.4980
   chunk 71 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 38 optimal weight:   20.0000
   chunk 73 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 54 optimal weight:    8.9990
   chunk 85 optimal weight:   10.0000
   overall best weight:    3.4988

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
A  87 ASN
A 131 ASN
A 186 GLN
A 204 ASN
A 322 GLN
A 339 ASN
B  77 HIS
B 252 ASN
B 296 ASN
B 377 ASN
B 403 ASN
B 412 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.118738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.096632 restraints weight = 14717.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 1.75
r_work: 0.3088 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  10291  Z= 0.317
  Angle     :  0.570  11.333  14586  Z= 0.314
  Chirality :  0.041   0.223   1679
  Planarity :  0.004   0.035   1310
  Dihedral  : 20.486  74.591   3088
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  3.88 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 15.57 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.29), residues: 799
  helix:  1.06 (0.28), residues: 363
  sheet: -0.34 (0.40), residues: 151
  loop : -1.65 (0.33), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  43 
 HIS   0.006   0.001   HIS A  72 
 PHE   0.015   0.002   PHE A 389 
 TYR   0.020   0.002   TYR A 351 
 ARG   0.006   0.001   ARG A 298 

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

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

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 168
  time to evaluate  : 0.842 
Fit side-chains
REVERT: A   25 ARG cc_start: 0.8293 (mtp85) cc_final: 0.8054 (mpt90)
REVERT: A   30 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7976 (mt-10)
REVERT: A  141 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8431 (m-30)
REVERT: A  221 ILE cc_start: 0.8927 (mt) cc_final: 0.8704 (mp)
REVERT: A  222 MET cc_start: 0.9111 (ttp) cc_final: 0.8893 (ttp)
REVERT: A  242 ARG cc_start: 0.8492 (ptp90) cc_final: 0.8179 (ptp90)
REVERT: A  244 LYS cc_start: 0.8841 (pttt) cc_final: 0.8625 (pttt)
REVERT: A  264 MET cc_start: 0.8419 (mtt) cc_final: 0.8095 (mtp)
REVERT: A  344 ASP cc_start: 0.8103 (t0) cc_final: 0.7814 (t70)
REVERT: A  377 ASN cc_start: 0.8551 (t0) cc_final: 0.7570 (p0)
REVERT: B   71 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8412 (p)
REVERT: B  199 ASN cc_start: 0.8467 (t0) cc_final: 0.8261 (t0)
REVERT: B  208 ASP cc_start: 0.7532 (t0) cc_final: 0.7321 (t0)
REVERT: B  222 MET cc_start: 0.8690 (ttp) cc_final: 0.8204 (ttt)
REVERT: B  242 ARG cc_start: 0.8474 (ptp-170) cc_final: 0.7641 (ptp-170)
REVERT: B  264 MET cc_start: 0.7479 (tpp) cc_final: 0.7263 (mpp)
REVERT: B  316 MET cc_start: 0.8515 (mmm) cc_final: 0.8270 (mmm)
REVERT: B  339 ASN cc_start: 0.8484 (t0) cc_final: 0.8215 (t0)
  outliers start: 21
  outliers final: 5
  residues processed: 183
  average time/residue: 1.7473
  time to fit residues: 336.0492
Evaluate side-chains
  177 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 170
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  262 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 82 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 22 optimal weight:    9.9990
   chunk 63 optimal weight:    0.8980
   chunk 30 optimal weight:    8.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  56 HIS
A 204 ASN
B 407 ASN
B 412 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.121029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.098796 restraints weight = 14968.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 1.76
r_work: 0.3124 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10291  Z= 0.192
  Angle     :  0.523  10.553  14586  Z= 0.286
  Chirality :  0.037   0.215   1679
  Planarity :  0.003   0.034   1310
  Dihedral  : 20.365  73.659   3083
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  2.88 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 17.43 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.29), residues: 799
  helix:  1.57 (0.28), residues: 364
  sheet: -0.26 (0.40), residues: 157
  loop : -1.64 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  43 
 HIS   0.003   0.001   HIS A  72 
 PHE   0.012   0.002   PHE B 389 
 TYR   0.014   0.001   TYR A 351 
 ARG   0.006   0.000   ARG B 406 

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

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

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 174
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 ASP cc_start: 0.7979 (t0) cc_final: 0.7744 (t70)
REVERT: A  141 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8400 (m-30)
REVERT: A  177 MET cc_start: 0.9053 (tpp) cc_final: 0.8504 (tpt)
REVERT: A  221 ILE cc_start: 0.8937 (mt) cc_final: 0.8698 (mp)
REVERT: A  222 MET cc_start: 0.9149 (ttp) cc_final: 0.8906 (ttp)
REVERT: A  242 ARG cc_start: 0.8487 (ptp90) cc_final: 0.8083 (ptp90)
REVERT: A  244 LYS cc_start: 0.8844 (pttt) cc_final: 0.8617 (pttt)
REVERT: A  312 MET cc_start: 0.8687 (mmp) cc_final: 0.8172 (mmt)
REVERT: A  344 ASP cc_start: 0.8051 (t0) cc_final: 0.7764 (t70)
REVERT: A  354 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7879 (mp0)
REVERT: A  377 ASN cc_start: 0.8420 (t0) cc_final: 0.7459 (p0)
REVERT: B  174 LYS cc_start: 0.8595 (tppp) cc_final: 0.8389 (tppp)
REVERT: B  199 ASN cc_start: 0.8562 (t0) cc_final: 0.8208 (t0)
REVERT: B  222 MET cc_start: 0.8701 (ttp) cc_final: 0.8499 (ttt)
REVERT: B  339 ASN cc_start: 0.8523 (t0) cc_final: 0.8258 (t0)
REVERT: B  407 ASN cc_start: 0.7415 (m-40) cc_final: 0.7089 (m-40)
  outliers start: 21
  outliers final: 5
  residues processed: 184
  average time/residue: 1.7423
  time to fit residues: 336.7731
Evaluate side-chains
  173 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 166
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  370 GLN
Chi-restraints excluded: chain B residue  160 LYS
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  239 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 61 optimal weight:   10.0000
   chunk 79 optimal weight:    6.9990
   chunk 44 optimal weight:    6.9990
   chunk 28 optimal weight:    7.9990
   chunk 41 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   chunk 16 optimal weight:    8.9990
   chunk 40 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    8.9990
   overall best weight:    4.7588

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

Flipped N/Q/H residues before XYZ refinement:
B 412 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.117277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.095080 restraints weight = 14946.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 1.76
r_work: 0.3064 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060  10291  Z= 0.408
  Angle     :  0.593  10.745  14586  Z= 0.324
  Chirality :  0.042   0.230   1679
  Planarity :  0.004   0.034   1310
  Dihedral  : 20.430  73.772   3082
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  3.88 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.71 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.29), residues: 799
  helix:  1.60 (0.28), residues: 363
  sheet: -0.17 (0.40), residues: 151
  loop : -1.64 (0.33), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  43 
 HIS   0.007   0.002   HIS A  72 
 PHE   0.016   0.002   PHE A 102 
 TYR   0.019   0.002   TYR A 351 
 ARG   0.009   0.001   ARG B 406 

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

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

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 177
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 MET cc_start: 0.9109 (ttp) cc_final: 0.8862 (ttp)
REVERT: A  234 MET cc_start: 0.8989 (mtp) cc_final: 0.8787 (mtp)
REVERT: A  244 LYS cc_start: 0.8874 (pttt) cc_final: 0.8648 (pttt)
REVERT: A  283 ARG cc_start: 0.8678 (tpp-160) cc_final: 0.8428 (tpt170)
REVERT: A  344 ASP cc_start: 0.8079 (t0) cc_final: 0.7824 (t70)
REVERT: A  377 ASN cc_start: 0.8490 (t0) cc_final: 0.7501 (p0)
REVERT: B  142 TYR cc_start: 0.8403 (m-80) cc_final: 0.7975 (m-10)
REVERT: B  199 ASN cc_start: 0.8542 (t0) cc_final: 0.8161 (t0)
REVERT: B  254 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7764 (mtp85)
REVERT: B  264 MET cc_start: 0.7652 (tpp) cc_final: 0.7376 (mpp)
REVERT: B  339 ASN cc_start: 0.8468 (t0) cc_final: 0.8088 (t0)
REVERT: B  406 ARG cc_start: 0.7109 (mtp85) cc_final: 0.6682 (ttt90)
REVERT: B  407 ASN cc_start: 0.7255 (m-40) cc_final: 0.6907 (m110)
  outliers start: 20
  outliers final: 11
  residues processed: 186
  average time/residue: 1.8340
  time to fit residues: 357.5086
Evaluate side-chains
  185 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 174
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LYS
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  370 GLN
Chi-restraints excluded: chain B residue  160 LYS
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  325 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 46 optimal weight:    8.9990
   chunk 78 optimal weight:    6.9990
   chunk 61 optimal weight:    8.9990
   chunk 71 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 29 optimal weight:    8.9990
   chunk 80 optimal weight:    4.9990
   chunk 55 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 194 HIS
** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 412 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.117445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.095221 restraints weight = 14867.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.76
r_work: 0.3066 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  10291  Z= 0.391
  Angle     :  0.590  10.443  14586  Z= 0.323
  Chirality :  0.042   0.242   1679
  Planarity :  0.004   0.034   1310
  Dihedral  : 20.418  73.788   3082
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.13 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 20.71 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.30), residues: 799
  helix:  1.67 (0.28), residues: 363
  sheet: -0.26 (0.38), residues: 157
  loop : -1.64 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  43 
 HIS   0.007   0.001   HIS A  72 
 PHE   0.015   0.002   PHE A 102 
 TYR   0.020   0.002   TYR A 351 
 ARG   0.007   0.001   ARG B  25 

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

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

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 175
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
REVERT: A  177 MET cc_start: 0.9056 (tpp) cc_final: 0.8511 (tpt)
REVERT: A  191 GLN cc_start: 0.8967 (mt0) cc_final: 0.8661 (mt0)
REVERT: A  221 ILE cc_start: 0.8907 (mt) cc_final: 0.8702 (mp)
REVERT: A  222 MET cc_start: 0.9100 (ttp) cc_final: 0.8826 (ttp)
REVERT: A  244 LYS cc_start: 0.8868 (pttt) cc_final: 0.8635 (pttt)
REVERT: A  264 MET cc_start: 0.8431 (mtt) cc_final: 0.7954 (mtp)
REVERT: A  267 GLN cc_start: 0.8402 (tm-30) cc_final: 0.7999 (tm-30)
REVERT: A  344 ASP cc_start: 0.8062 (t0) cc_final: 0.7815 (t70)
REVERT: A  346 GLN cc_start: 0.8623 (mt0) cc_final: 0.8382 (mt0)
REVERT: A  354 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7967 (mp0)
REVERT: A  377 ASN cc_start: 0.8455 (t0) cc_final: 0.7496 (p0)
REVERT: B  187 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8220 (m)
REVERT: B  199 ASN cc_start: 0.8543 (t0) cc_final: 0.8165 (t0)
REVERT: B  254 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7770 (mtp85)
REVERT: B  264 MET cc_start: 0.7612 (tpp) cc_final: 0.7358 (ttm)
REVERT: B  338 GLN cc_start: 0.8390 (mm110) cc_final: 0.8093 (mm110)
REVERT: B  339 ASN cc_start: 0.8478 (t0) cc_final: 0.8088 (t0)
REVERT: B  406 ARG cc_start: 0.7131 (mtp85) cc_final: 0.6892 (ttt90)
REVERT: B  407 ASN cc_start: 0.7409 (m-40) cc_final: 0.7109 (m110)
  outliers start: 24
  outliers final: 11
  residues processed: 187
  average time/residue: 1.8106
  time to fit residues: 355.0472
Evaluate side-chains
  190 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 177
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  174 LYS
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  370 GLN
Chi-restraints excluded: chain B residue   50 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  325 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0040
   chunk 46 optimal weight:    8.9990
   chunk 28 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   chunk 69 optimal weight:    9.9990
   chunk 50 optimal weight:    7.9990
   chunk 31 optimal weight:    0.8980
   chunk 72 optimal weight:    0.0070
   overall best weight:    0.7212

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

Flipped N/Q/H residues before XYZ refinement:
A 186 GLN
B 237 GLN
B 412 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.121996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.099871 restraints weight = 14834.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.75
r_work: 0.3142 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10291  Z= 0.150
  Angle     :  0.508  10.440  14586  Z= 0.279
  Chirality :  0.037   0.227   1679
  Planarity :  0.003   0.034   1310
  Dihedral  : 20.282  73.871   3082
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  3.63 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 22.43 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.30), residues: 799
  helix:  2.03 (0.28), residues: 364
  sheet: -0.03 (0.39), residues: 155
  loop : -1.46 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  17 
 HIS   0.002   0.001   HIS B  72 
 PHE   0.013   0.001   PHE A 389 
 TYR   0.013   0.001   TYR A 351 
 ARG   0.007   0.000   ARG B  25 

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

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

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 178
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 TYR cc_start: 0.9125 (m-80) cc_final: 0.8763 (m-80)
REVERT: A  221 ILE cc_start: 0.8928 (mt) cc_final: 0.8713 (mp)
REVERT: A  242 ARG cc_start: 0.8508 (ptp90) cc_final: 0.8276 (ptp90)
REVERT: A  244 LYS cc_start: 0.8870 (pttt) cc_final: 0.8615 (pttt)
REVERT: A  288 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7031 (mt-10)
REVERT: A  312 MET cc_start: 0.8638 (mmp) cc_final: 0.8331 (mmp)
REVERT: A  344 ASP cc_start: 0.7869 (t0) cc_final: 0.7583 (t70)
REVERT: A  354 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7366 (mp0)
REVERT: A  377 ASN cc_start: 0.8354 (t0) cc_final: 0.7443 (p0)
REVERT: B  142 TYR cc_start: 0.8367 (m-80) cc_final: 0.8138 (m-10)
REVERT: B  174 LYS cc_start: 0.8500 (tppp) cc_final: 0.8036 (tppp)
REVERT: B  199 ASN cc_start: 0.8571 (t0) cc_final: 0.8218 (t0)
REVERT: B  264 MET cc_start: 0.7523 (tpp) cc_final: 0.7284 (ttm)
REVERT: B  338 GLN cc_start: 0.8375 (mm110) cc_final: 0.8130 (mm110)
REVERT: B  339 ASN cc_start: 0.8483 (t0) cc_final: 0.8154 (t0)
REVERT: B  406 ARG cc_start: 0.6898 (mtp85) cc_final: 0.6605 (ttt90)
REVERT: B  407 ASN cc_start: 0.7459 (m-40) cc_final: 0.7171 (m110)
  outliers start: 13
  outliers final: 5
  residues processed: 185
  average time/residue: 1.7979
  time to fit residues: 349.2029
Evaluate side-chains
  180 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 174
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  239 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 12 optimal weight:    8.9990
   chunk 48 optimal weight:   10.0000
   chunk 18 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 93 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 3 optimal weight:    0.6980
   chunk 30 optimal weight:   10.0000
   overall best weight:    2.8986

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

Flipped N/Q/H residues before XYZ refinement:
B 399 ASN
B 412 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.119509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.097201 restraints weight = 15010.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 1.77
r_work: 0.3094 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10291  Z= 0.272
  Angle     :  0.552  10.434  14586  Z= 0.299
  Chirality :  0.039   0.216   1679
  Planarity :  0.004   0.054   1310
  Dihedral  : 20.293  73.736   3082
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.13 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 23.86 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.30), residues: 799
  helix:  2.00 (0.28), residues: 365
  sheet: -0.01 (0.39), residues: 155
  loop : -1.48 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  43 
 HIS   0.005   0.001   HIS A  72 
 PHE   0.011   0.002   PHE A 389 
 TYR   0.017   0.001   TYR A 351 
 ARG   0.012   0.001   ARG A 121 

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

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

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 172
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
REVERT: A  221 ILE cc_start: 0.8945 (mt) cc_final: 0.8709 (mp)
REVERT: A  244 LYS cc_start: 0.8874 (pttt) cc_final: 0.8625 (pttt)
REVERT: A  288 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6997 (mt-10)
REVERT: A  312 MET cc_start: 0.8622 (mmp) cc_final: 0.8265 (mmp)
REVERT: A  344 ASP cc_start: 0.8031 (t0) cc_final: 0.7746 (t70)
REVERT: A  377 ASN cc_start: 0.8326 (t0) cc_final: 0.7422 (p0)
REVERT: B   11 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8753 (pttt)
REVERT: B  199 ASN cc_start: 0.8560 (t0) cc_final: 0.8198 (t0)
REVERT: B  264 MET cc_start: 0.7574 (tpp) cc_final: 0.7332 (ttm)
REVERT: B  338 GLN cc_start: 0.8431 (mm110) cc_final: 0.8153 (mm110)
REVERT: B  339 ASN cc_start: 0.8497 (t0) cc_final: 0.8166 (t0)
REVERT: B  406 ARG cc_start: 0.6889 (mtp85) cc_final: 0.6528 (ttt90)
  outliers start: 14
  outliers final: 9
  residues processed: 178
  average time/residue: 1.7847
  time to fit residues: 333.1730
Evaluate side-chains
  185 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 175
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  370 GLN
Chi-restraints excluded: chain B residue   11 LYS
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  239 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 50 optimal weight:    8.9990
   chunk 88 optimal weight:    8.9990
   chunk 51 optimal weight:   10.0000
   chunk 83 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 44 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
B 399 ASN
B 412 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.117426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.095155 restraints weight = 15073.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 1.80
r_work: 0.3060 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056  10291  Z= 0.413
  Angle     :  0.625  11.807  14586  Z= 0.337
  Chirality :  0.043   0.231   1679
  Planarity :  0.004   0.037   1310
  Dihedral  : 20.356  73.764   3082
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.38 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 23.86 %
    Favored  : 73.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.29), residues: 799
  helix:  1.75 (0.28), residues: 365
  sheet: -0.07 (0.39), residues: 157
  loop : -1.60 (0.34), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  43 
 HIS   0.007   0.002   HIS A  72 
 PHE   0.016   0.002   PHE A 102 
 TYR   0.032   0.002   TYR B 351 
 ARG   0.008   0.001   ARG B  25 

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

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

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 178
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 MET cc_start: 0.9065 (tpp) cc_final: 0.8638 (tpt)
REVERT: A  221 ILE cc_start: 0.8955 (mt) cc_final: 0.8719 (mp)
REVERT: A  244 LYS cc_start: 0.8894 (pttt) cc_final: 0.8658 (pttt)
REVERT: A  344 ASP cc_start: 0.8081 (t0) cc_final: 0.7815 (t70)
REVERT: A  377 ASN cc_start: 0.8438 (t0) cc_final: 0.7465 (p0)
REVERT: B  107 LYS cc_start: 0.8602 (mmmm) cc_final: 0.8183 (mmmm)
REVERT: B  187 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8158 (m)
REVERT: B  199 ASN cc_start: 0.8538 (t0) cc_final: 0.8142 (t0)
REVERT: B  264 MET cc_start: 0.7685 (tpp) cc_final: 0.7374 (ttm)
REVERT: B  338 GLN cc_start: 0.8459 (mm110) cc_final: 0.8168 (mm110)
REVERT: B  339 ASN cc_start: 0.8483 (t0) cc_final: 0.8146 (t0)
REVERT: B  406 ARG cc_start: 0.7021 (mtp85) cc_final: 0.6556 (ttt90)
  outliers start: 18
  outliers final: 10
  residues processed: 185
  average time/residue: 1.8359
  time to fit residues: 355.8134
Evaluate side-chains
  186 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 175
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  370 GLN
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  315 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   chunk 45 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 71 optimal weight:    6.9990
   chunk 73 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 186 GLN
B 399 ASN
B 412 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.119061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.096839 restraints weight = 14994.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 1.76
r_work: 0.3091 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10291  Z= 0.280
  Angle     :  0.567  10.469  14586  Z= 0.310
  Chirality :  0.040   0.232   1679
  Planarity :  0.004   0.035   1310
  Dihedral  : 20.284  73.727   3080
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  3.88 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 24.86 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.30), residues: 799
  helix:  1.89 (0.28), residues: 365
  sheet: -0.06 (0.39), residues: 157
  loop : -1.56 (0.34), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 340 
 HIS   0.005   0.001   HIS A  72 
 PHE   0.013   0.002   PHE A 389 
 TYR   0.019   0.001   TYR A  84 
 ARG   0.008   0.001   ARG B  25 

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

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

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 173
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 ILE cc_start: 0.8959 (mt) cc_final: 0.8725 (mp)
REVERT: A  242 ARG cc_start: 0.8571 (ptp90) cc_final: 0.8259 (ptp90)
REVERT: A  244 LYS cc_start: 0.8882 (pttt) cc_final: 0.8632 (pttt)
REVERT: A  264 MET cc_start: 0.8437 (mtt) cc_final: 0.8004 (mtp)
REVERT: A  312 MET cc_start: 0.8661 (mmp) cc_final: 0.8244 (mmp)
REVERT: A  344 ASP cc_start: 0.8048 (t0) cc_final: 0.7787 (t70)
REVERT: A  377 ASN cc_start: 0.8332 (t0) cc_final: 0.7432 (p0)
REVERT: B    8 GLU cc_start: 0.7974 (tt0) cc_final: 0.7774 (tp30)
REVERT: B  187 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8123 (m)
REVERT: B  199 ASN cc_start: 0.8568 (t0) cc_final: 0.8368 (t0)
REVERT: B  220 LYS cc_start: 0.8603 (mttt) cc_final: 0.8098 (mtmp)
REVERT: B  264 MET cc_start: 0.7649 (tpp) cc_final: 0.7345 (ttm)
REVERT: B  312 MET cc_start: 0.8314 (mmp) cc_final: 0.8094 (mmm)
REVERT: B  338 GLN cc_start: 0.8451 (mm110) cc_final: 0.8154 (mm110)
REVERT: B  339 ASN cc_start: 0.8490 (t0) cc_final: 0.8176 (t0)
REVERT: B  406 ARG cc_start: 0.7024 (mtp85) cc_final: 0.6624 (ttt90)
  outliers start: 14
  outliers final: 9
  residues processed: 181
  average time/residue: 1.8211
  time to fit residues: 345.2852
Evaluate side-chains
  182 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 172
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  370 GLN
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  239 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 45 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 69 optimal weight:    8.9990
   chunk 71 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 89 optimal weight:    0.6980
   chunk 25 optimal weight:   10.0000
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
B 399 ASN
B 412 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.119806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.097520 restraints weight = 14973.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 1.76
r_work: 0.3100 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10291  Z= 0.252
  Angle     :  0.568  10.508  14586  Z= 0.309
  Chirality :  0.039   0.224   1679
  Planarity :  0.004   0.057   1310
  Dihedral  : 20.261  73.742   3080
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.01 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 25.43 %
    Favored  : 72.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.30), residues: 799
  helix:  1.94 (0.28), residues: 364
  sheet: -0.07 (0.39), residues: 155
  loop : -1.39 (0.35), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 340 
 HIS   0.004   0.001   HIS B 194 
 PHE   0.012   0.002   PHE A 389 
 TYR   0.029   0.001   TYR B 351 
 ARG   0.016   0.001   ARG A 121 

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

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

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1598 Ramachandran restraints generated.
    799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 173
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 ILE cc_start: 0.8939 (mt) cc_final: 0.8690 (mp)
REVERT: A  244 LYS cc_start: 0.8830 (pttt) cc_final: 0.8586 (pttt)
REVERT: A  264 MET cc_start: 0.8417 (mtt) cc_final: 0.7992 (mtp)
REVERT: A  312 MET cc_start: 0.8659 (mmp) cc_final: 0.8241 (mmt)
REVERT: A  344 ASP cc_start: 0.7893 (t0) cc_final: 0.7620 (t70)
REVERT: A  377 ASN cc_start: 0.8357 (t0) cc_final: 0.7465 (p0)
REVERT: B  187 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8106 (m)
REVERT: B  199 ASN cc_start: 0.8569 (t0) cc_final: 0.8189 (t0)
REVERT: B  264 MET cc_start: 0.7697 (tpp) cc_final: 0.7399 (ttm)
REVERT: B  312 MET cc_start: 0.8283 (mmp) cc_final: 0.8055 (mmm)
REVERT: B  338 GLN cc_start: 0.8454 (mm110) cc_final: 0.8159 (mm110)
REVERT: B  339 ASN cc_start: 0.8476 (t0) cc_final: 0.8157 (t0)
REVERT: B  406 ARG cc_start: 0.6983 (mtp85) cc_final: 0.6673 (ttt90)
  outliers start: 12
  outliers final: 9
  residues processed: 178
  average time/residue: 1.8315
  time to fit residues: 341.4190
Evaluate side-chains
  182 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 172
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  370 GLN
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  239 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 93 optimal weight:    5.9990
   chunk 32 optimal weight:    8.9990
   chunk 23 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 46 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 33 optimal weight:    0.0270
   chunk 13 optimal weight:   10.0000
   chunk 52 optimal weight:   10.0000
   chunk 54 optimal weight:    7.9990
   overall best weight:    4.0044

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
B 399 ASN
B 412 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.118232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.095915 restraints weight = 15025.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 1.77
r_work: 0.3078 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  10291  Z= 0.357
  Angle     :  0.611   9.994  14586  Z= 0.331
  Chirality :  0.041   0.229   1679
  Planarity :  0.004   0.038   1310
  Dihedral  : 20.308  73.786   3080
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.51 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 25.00 %
    Favored  : 72.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.29), residues: 799
  helix:  1.82 (0.28), residues: 365
  sheet: -0.16 (0.38), residues: 157
  loop : -1.57 (0.34), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 340 
 HIS   0.006   0.001   HIS A  72 
 PHE   0.013   0.002   PHE A 102 
 TYR   0.019   0.002   TYR A 351 
 ARG   0.008   0.001   ARG B  25 

===============================================================================
Job complete
usr+sys time: 8536.70 seconds
wall clock time: 150 minutes 54.84 seconds (9054.84 seconds total)