Starting phenix.real_space_refine
on Sun Jun  8 16:10:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j3r_35965/06_2025/8j3r_35965.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j3r_35965/06_2025/8j3r_35965.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j3r_35965/06_2025/8j3r_35965.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j3r_35965/06_2025/8j3r_35965.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j3r_35965/06_2025/8j3r_35965.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j3r_35965/06_2025/8j3r_35965.cif"
  }
  resolution = 2.95
  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=   0.076
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      1      6.06       5
     P     140      5.49       5
     Mg      3      5.21       5
     S      32      5.16       5
     C    5481      2.51       5
     N    1731      2.21       5
     O    2138      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9526
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3429
          Classifications: {'peptide': 422}
          Link IDs: {'PTRANS': 10, 'TRANS': 411}
    Chain: "D"
      Number of atoms: 466
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 466
          Classifications: {'DNA': 23}
          Link IDs: {'rna3p': 22}
    Chain: "E"
      Number of atoms: 166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 166
          Classifications: {'DNA': 8}
          Link IDs: {'rna3p': 7}
    Chain: "C"
      Number of atoms: 2345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 2345
          Classifications: {'RNA': 109}
          Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 2, 'rna3p_pur': 56, 'rna3p_pyr': 41}
          Link IDs: {'rna2p': 12, 'rna3p': 96}
    Chain: "B"
      Number of atoms: 3116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 387, 3116
          Classifications: {'peptide': 387}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 9, 'TRANS': 377}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 19
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 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}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3055  SG  CYS A 372      88.301  55.825  32.384  1.00103.10           S
  ATOM   3076  SG  CYS A 375      91.722  54.642  33.836  1.00 97.25           S
  ATOM   3193  SG  CYS A 391      90.472  58.181  34.340  1.00116.70           S
  ATOM   3215  SG  CYS A 394      91.398  56.126  32.490  1.00100.31           S

  Time building chain proxies: 6.25, per 1000 atoms: 0.66
  Number of scatterers: 9526
  At special positions: 0
  Unit cell: (102.3, 117.7, 113.3, 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      1     29.99
     S      32     16.00
     P     140     15.00
     Mg      3     11.99
     O    2138      8.00
     N    1731      7.00
     C    5481      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: 2.46
  Conformation dependent library (CDL) restraints added in 761.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 394 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 391 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 372 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 375 "
      Number of angles added : 6


  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1516

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 8 sheets defined
      49.3% alpha, 17.6% beta
      46 base pairs and 86 stacking pairs defined.
    Time for finding SS restraints: 4.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 57
    Processing helix  chain 'A' and resid 61 through 66
    Processing helix  chain 'A' and resid 70 through 80
      removed outlier: 3.628A  pdb=" N   TYR A  74 " --> pdb=" O   ASN A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 105
      removed outlier: 3.638A  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 150 through 157
    Processing helix  chain 'A' and resid 171 through 183
      removed outlier: 4.060A  pdb=" N   THR A 175 " --> pdb=" O   GLY A 171 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE A 176 " --> pdb=" O   ALA A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 199
    Processing helix  chain 'A' and resid 247 through 268
      removed outlier: 3.759A  pdb=" N   GLU A 251 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASN A 252 " --> pdb=" O   GLY A 248 " (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 279 through 284
      removed outlier: 3.632A  pdb=" N   ARG A 283 " --> pdb=" O   GLY A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 316
    Processing helix  chain 'A' and resid 341 through 356
      removed outlier: 3.569A  pdb=" N   ALA A 356 " --> pdb=" O   LYS A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 409
    Processing helix  chain 'A' and resid 412 through 420
    Processing helix  chain 'B' and resid 16 through 46
    Processing helix  chain 'B' and resid 50 through 56
      removed outlier: 4.153A  pdb=" N   ASP B  54 " --> pdb=" O   SER B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 81
      removed outlier: 3.547A  pdb=" N   HIS B  77 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR B  78 " --> pdb=" O   TYR B  74 " (cutoff:3.500A)
      removed outlier: 3.750A  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 157
    Processing helix  chain 'B' and resid 171 through 183
    Processing helix  chain 'B' and resid 247 through 265
    Processing helix  chain 'B' and resid 286 through 317
    Processing helix  chain 'B' and resid 341 through 356
      removed outlier: 3.553A  pdb=" N   GLU B 355 " --> pdb=" O   TYR B 351 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA B 356 " --> pdb=" O   LYS B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 410
      removed outlier: 3.808A  pdb=" N   ILE B 410 " --> pdb=" O   ARG B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 420
      removed outlier: 3.851A  pdb=" N   ALA B 418 " --> pdb=" O   ASP B 414 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   SER B 420 " --> pdb=" O   ILE B 416 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 127
      removed outlier: 3.507A  pdb=" N   GLN A 191 " --> pdb=" O   ASN A 204 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS A 200 " --> pdb=" O   LYS A 195 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   TRP A 201 " --> pdb=" O   ILE A   9 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ILE A 166 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   SER A 164 " --> pdb=" O   PRO A  12 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   TYR A 142 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 127
      removed outlier: 3.507A  pdb=" N   GLN A 191 " --> pdb=" O   ASN A 204 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS A 200 " --> pdb=" O   LYS A 195 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 245
      removed outlier: 3.521A  pdb=" N   ALA A 232 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   MET A 222 " --> pdb=" O   GLN A 322 " (cutoff:3.500A)
      removed outlier: 8.397A  pdb=" N   GLU A 324 " --> pdb=" O   MET A 222 " (cutoff:3.500A)
      removed outlier: 8.742A  pdb=" N   ILE A 224 " --> pdb=" O   GLU A 324 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   ILE A 321 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   ILE A 363 " --> pdb=" O   ILE A 321 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   MET A 323 " --> pdb=" O   ILE A 363 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 388 through 390
      removed outlier: 3.638A  pdb=" N   ALA A 398 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 5
      removed outlier: 3.514A  pdb=" N   ALA B 189 " --> pdb=" O   SER B 206 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   ARG B 208 " --> pdb=" O   VAL B 187 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   VAL B 187 " --> pdb=" O   ARG B 208 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 12
      removed outlier: 6.756A  pdb=" N   ILE B 166 " --> pdb=" O   VAL B  10 " (cutoff:3.500A)
      removed outlier: 7.558A  pdb=" N   SER B 164 " --> pdb=" O   PRO B  12 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   TYR B 142 " --> pdb=" O   ILE B 167 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 242 through 245
      removed outlier: 7.169A  pdb=" N   LEU B 218 " --> pdb=" O   CYS B 318 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   THR B 320 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   LYS B 220 " --> pdb=" O   THR B 320 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   GLN B 322 " --> pdb=" O   LYS B 220 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   MET B 222 " --> pdb=" O   GLN B 322 " (cutoff:3.500A)
      removed outlier: 8.324A  pdb=" N   GLU B 324 " --> pdb=" O   MET B 222 " (cutoff:3.500A)
      removed outlier: 8.620A  pdb=" N   ILE B 224 " --> pdb=" O   GLU B 324 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 388 through 390

    356 hydrogen bonds defined for protein.
    1026 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      114 hydrogen bonds
      212 hydrogen bond angles
      0 basepair planarities
      46 basepair parallelities
      86 stacking parallelities
  Total time for adding SS restraints: 3.63

  Time building geometry restraints manager: 2.90 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: 2190
        1.33 -     1.45: 2776
        1.45 -     1.57: 4700
        1.57 -     1.69: 277
        1.69 -     1.81: 54
  Bond restraints: 9997
  Sorted by residual:
  bond pdb=" CA  ILE A 163 "
       pdb=" CB  ILE A 163 "
    ideal  model  delta    sigma   weight residual
    1.530  1.542 -0.012 1.11e-02 8.12e+03 1.19e+00
  bond pdb=" CA  ILE A 410 "
       pdb=" CB  ILE A 410 "
    ideal  model  delta    sigma   weight residual
    1.537  1.525  0.013 1.29e-02 6.01e+03 9.67e-01
  bond pdb=" CB  PRO B 365 "
       pdb=" CG  PRO B 365 "
    ideal  model  delta    sigma   weight residual
    1.492  1.539 -0.047 5.00e-02 4.00e+02 8.95e-01
  bond pdb=" C1'  DT E  -7 "
       pdb=" N1   DT E  -7 "
    ideal  model  delta    sigma   weight residual
    1.490  1.518 -0.028 3.00e-02 1.11e+03 8.74e-01
  bond pdb=" CB  VAL A  10 "
       pdb=" CG2 VAL A  10 "
    ideal  model  delta    sigma   weight residual
    1.521  1.496  0.025 3.30e-02 9.18e+02 5.59e-01
  ... (remaining 9992 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 13872
        1.53 -     3.06: 248
        3.06 -     4.58: 17
        4.58 -     6.11: 4
        6.11 -     7.64: 2
  Bond angle restraints: 14143
  Sorted by residual:
  angle pdb=" C   ARG A 197 "
        pdb=" N   LYS A 198 "
        pdb=" CA  LYS A 198 "
      ideal   model   delta    sigma   weight residual
     121.54  127.03   -5.49 1.91e+00 2.74e-01 8.27e+00
  angle pdb=" C1'   U C -45 "
        pdb=" N1    U C -45 "
        pdb=" C2    U C -45 "
      ideal   model   delta    sigma   weight residual
     117.70  125.34   -7.64 3.00e+00 1.11e-01 6.48e+00
  angle pdb=" C2'   U C   6 "
        pdb=" C1'   U C   6 "
        pdb=" N1    U C   6 "
      ideal   model   delta    sigma   weight residual
     112.00  115.56   -3.56 1.50e+00 4.44e-01 5.64e+00
  angle pdb=" N   GLN A 338 "
        pdb=" CA  GLN A 338 "
        pdb=" C   GLN A 338 "
      ideal   model   delta    sigma   weight residual
     112.93  110.33    2.60 1.12e+00 7.97e-01 5.37e+00
  angle pdb=" N   ASN A 158 "
        pdb=" CA  ASN A 158 "
        pdb=" CB  ASN A 158 "
      ideal   model   delta    sigma   weight residual
     113.65  110.33    3.32 1.47e+00 4.63e-01 5.11e+00
  ... (remaining 14138 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 5076
       17.90 -    35.80: 534
       35.80 -    53.71: 264
       53.71 -    71.61: 171
       71.61 -    89.51: 33
  Dihedral angle restraints: 6078
    sinusoidal: 3711
      harmonic: 2367
  Sorted by residual:
  dihedral pdb=" CA  LYS A  11 "
           pdb=" C   LYS A  11 "
           pdb=" N   PRO A  12 "
           pdb=" CA  PRO A  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.90   17.10     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  ASN A 131 "
           pdb=" CB  ASN A 131 "
           pdb=" CG  ASN A 131 "
           pdb=" OD1 ASN A 131 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -168.80  -71.20     2      2.00e+01 2.50e-03 1.08e+01
  dihedral pdb=" CA  ASP B 364 "
           pdb=" CB  ASP B 364 "
           pdb=" CG  ASP B 364 "
           pdb=" OD1 ASP B 364 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.06   56.06     1      2.00e+01 2.50e-03 1.06e+01
  ... (remaining 6075 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1234
       0.035 -    0.069: 277
       0.069 -    0.104: 87
       0.104 -    0.138: 27
       0.138 -    0.173: 3
  Chirality restraints: 1628
  Sorted by residual:
  chirality pdb=" C1'   G C -83 "
            pdb=" O4'   G C -83 "
            pdb=" C2'   G C -83 "
            pdb=" N9    G C -83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.28    0.17 2.00e-01 2.50e+01 7.47e-01
  chirality pdb=" CA  ILE A 116 "
            pdb=" N   ILE A 116 "
            pdb=" C   ILE A 116 "
            pdb=" CB  ILE A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.37e-01
  chirality pdb=" C1'   U C -49 "
            pdb=" O4'   U C -49 "
            pdb=" C2'   U C -49 "
            pdb=" N1    U C -49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.32    0.14 2.00e-01 2.50e+01 5.13e-01
  ... (remaining 1625 not shown)

  Planarity restraints: 1293
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U C   6 "   -0.030 2.00e-02 2.50e+03   1.51e-02 5.12e+00
        pdb=" N1    U C   6 "    0.032 2.00e-02 2.50e+03
        pdb=" C2    U C   6 "    0.004 2.00e-02 2.50e+03
        pdb=" O2    U C   6 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    U C   6 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    U C   6 "   -0.003 2.00e-02 2.50e+03
        pdb=" O4    U C   6 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5    U C   6 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    U C   6 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C -44 "   -0.028 2.00e-02 2.50e+03   1.16e-02 4.04e+00
        pdb=" N9    G C -44 "    0.026 2.00e-02 2.50e+03
        pdb=" C8    G C -44 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    G C -44 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G C -44 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G C -44 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6    G C -44 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1    G C -44 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    G C -44 "    0.002 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 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C   7 "   -0.026 2.00e-02 2.50e+03   1.18e-02 3.86e+00
        pdb=" N9    A C   7 "    0.028 2.00e-02 2.50e+03
        pdb=" C8    A C   7 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    A C   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    A C   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A C   7 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A C   7 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A C   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    A C   7 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    A C   7 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A C   7 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1290 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 117
        2.63 -     3.20: 7902
        3.20 -     3.76: 16080
        3.76 -     4.33: 22344
        4.33 -     4.90: 33220
  Nonbonded interactions: 79663
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 334 "
            pdb="MG    MG A 502 "
     model   vdw
     2.060 2.170
  nonbonded pdb=" NE2 GLN B 322 "
            pdb=" O   ILE B 408 "
     model   vdw
     2.229 3.120
  nonbonded pdb=" O   LEU B 337 "
            pdb=" OH  TYR B 342 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O2'   U C -45 "
            pdb=" NZ  LYS B 129 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" O2'   A C -66 "
            pdb=" OE2 GLU B 108 "
     model   vdw
     2.266 3.040
  ... (remaining 79658 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 81 or (resid 82 through 8 \ 
3 and (name N or name CA or name C or name O or name CB )) or resid 84 through 1 \ 
60 or (resid 161 and (name N or name CA or name C or name O or name CB )) or res \ 
id 162 through 219 or (resid 220 and (name N or name CA or name C or name O or n \ 
ame CB )) or resid 221 through 224 or (resid 225 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 226 through 243 or (resid 244 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 245 through 257 or (resid 258 \ 
 and (name N or name CA or name C or name O or name CB )) or resid 259 through 2 \ 
65 or resid 285 through 326 or resid 331 or (resid 332 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 333 through 365 or (resid 366 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 367 through 378 or (res \ 
id 379 and (name N or name CA or name C or name O or name CB )) or resid 385 thr \ 
ough 414 or (resid 415 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 416 through 421))
  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:             0.160
  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:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     28.980
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4967
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      :  0.003   0.071  10001  Z= 0.131
  Angle     :  0.765  56.945  14149  Z= 0.307
  Chirality :  0.036   0.173   1628
  Planarity :  0.003   0.034   1293
  Dihedral  : 20.205  89.510   4562
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 11.01 %
    Favored  : 86.52 %
  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:  0.87 (0.29), residues: 797
  helix:  1.90 (0.26), residues: 361
  sheet:  0.11 (0.39), residues: 162
  loop : -0.90 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  43 
 HIS   0.003   0.001   HIS A 303 
 PHE   0.007   0.001   PHE B 102 
 TYR   0.011   0.001   TYR A 119 
 ARG   0.002   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22544 (  462)
  hydrogen bonds       : angle       6.19927 ( 1238)
  metal coordination   : bond        0.03778 (    4)
  metal coordination   : angle      28.09070 (    6)
  covalent geometry    : bond        0.00262 ( 9997)
  covalent geometry    : angle       0.50010 (14143)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 ASN cc_start: 0.6649 (OUTLIER) cc_final: 0.6447 (m110)
REVERT: A  377 ASN cc_start: 0.6732 (t0) cc_final: 0.6497 (t0)
REVERT: B  141 ASP cc_start: 0.6652 (OUTLIER) cc_final: 0.6234 (m-30)
REVERT: B  142 TYR cc_start: 0.2634 (m-80) cc_final: 0.1486 (m-80)
REVERT: B  288 GLU cc_start: 0.4753 (OUTLIER) cc_final: 0.4004 (tm-30)
  outliers start: 17
  outliers final: 2
  residues processed: 164
  average time/residue: 1.2452
  time to fit residues: 217.9445
Evaluate side-chains
  113 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 ASN
Chi-restraints excluded: chain B residue  141 ASP
Chi-restraints excluded: chain B residue  236 PHE
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  320 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0020
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 47 optimal weight:    8.9990
   chunk 37 optimal weight:    0.8980
   chunk 72 optimal weight:    7.9990
   chunk 27 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 83 optimal weight:    6.9990
   overall best weight:    1.9794

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

Flipped N/Q/H residues before XYZ refinement:
B  29 GLN
B  77 HIS
B 194 HIS
B 403 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.151674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.125801 restraints weight = 15561.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 1.99
r_work: 0.3514 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.7546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075  10001  Z= 0.286
  Angle     :  0.826  10.551  14149  Z= 0.442
  Chirality :  0.046   0.174   1628
  Planarity :  0.006   0.054   1293
  Dihedral  : 21.930  85.572   2941
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 16.52 %
    Favored  : 79.71 %
  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: -0.14 (0.28), residues: 797
  helix:  1.04 (0.25), residues: 378
  sheet: -0.66 (0.39), residues: 140
  loop : -1.30 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP B  43 
 HIS   0.008   0.003   HIS A 139 
 PHE   0.026   0.004   PHE A 253 
 TYR   0.019   0.003   TYR B 202 
 ARG   0.014   0.001   ARG B 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05521 (  462)
  hydrogen bonds       : angle       4.55060 ( 1238)
  metal coordination   : bond        0.01071 (    4)
  metal coordination   : angle       3.74604 (    6)
  covalent geometry    : bond        0.00580 ( 9997)
  covalent geometry    : angle       0.82276 (14143)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 207
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.9040 (ptpt) cc_final: 0.8824 (ptmt)
REVERT: A   14 ASP cc_start: 0.7451 (t0) cc_final: 0.7141 (t70)
REVERT: A   82 LYS cc_start: 0.8094 (mttt) cc_final: 0.7853 (mttt)
REVERT: A  100 ASP cc_start: 0.7793 (m-30) cc_final: 0.7353 (m-30)
REVERT: A  120 LYS cc_start: 0.8006 (pttt) cc_final: 0.7759 (pttt)
REVERT: A  288 GLU cc_start: 0.7140 (tm-30) cc_final: 0.6917 (tm-30)
REVERT: A  294 ILE cc_start: 0.8707 (mt) cc_final: 0.8404 (mp)
REVERT: A  323 MET cc_start: 0.8402 (mtm) cc_final: 0.8197 (mtm)
REVERT: A  332 ILE cc_start: 0.6716 (OUTLIER) cc_final: 0.6456 (pp)
REVERT: A  351 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6539 (t80)
REVERT: A  366 GLN cc_start: 0.7392 (tt0) cc_final: 0.7174 (tp-100)
REVERT: B  196 ASP cc_start: 0.5407 (OUTLIER) cc_final: 0.4966 (p0)
REVERT: B  312 MET cc_start: 0.7025 (mmm) cc_final: 0.6203 (mmt)
REVERT: B  323 MET cc_start: 0.3931 (ptm) cc_final: 0.3728 (ptm)
REVERT: B  355 GLU cc_start: 0.6121 (mt-10) cc_final: 0.5746 (mt-10)
  outliers start: 26
  outliers final: 7
  residues processed: 219
  average time/residue: 1.3293
  time to fit residues: 310.6397
Evaluate side-chains
  174 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 164
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain B residue  320 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 47 optimal weight:    8.9990
   chunk 54 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 50 optimal weight:    8.9990
   chunk 52 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 347 GLN
** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.144115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.116187 restraints weight = 15245.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.01
r_work: 0.3342 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.9749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10001  Z= 0.171
  Angle     :  0.622  11.027  14149  Z= 0.329
  Chirality :  0.040   0.168   1628
  Planarity :  0.005   0.051   1293
  Dihedral  : 21.705  89.836   2932
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 24.35 %
    Favored  : 71.74 %
  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:  0.93 (0.28), residues: 797
  helix:  2.17 (0.25), residues: 371
  sheet:  0.01 (0.39), residues: 157
  loop : -1.26 (0.34), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  17 
 HIS   0.009   0.001   HIS A 278 
 PHE   0.007   0.001   PHE A 253 
 TYR   0.034   0.002   TYR B 233 
 ARG   0.010   0.001   ARG A 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05183 (  462)
  hydrogen bonds       : angle       3.86923 ( 1238)
  metal coordination   : bond        0.00801 (    4)
  metal coordination   : angle       5.49381 (    6)
  covalent geometry    : bond        0.00367 ( 9997)
  covalent geometry    : angle       0.61220 (14143)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 197
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASP cc_start: 0.7669 (t0) cc_final: 0.7437 (t70)
REVERT: A   28 GLN cc_start: 0.8317 (mt0) cc_final: 0.7957 (mt0)
REVERT: A  105 TYR cc_start: 0.8614 (m-80) cc_final: 0.8360 (m-80)
REVERT: A  121 ARG cc_start: 0.7771 (ptm-80) cc_final: 0.7495 (ptm-80)
REVERT: A  134 VAL cc_start: 0.8207 (p) cc_final: 0.7969 (t)
REVERT: A  160 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8216 (ttpp)
REVERT: A  161 ARG cc_start: 0.7765 (mmt90) cc_final: 0.7462 (mtp85)
REVERT: A  197 ARG cc_start: 0.8733 (tmt90) cc_final: 0.8414 (ttp-170)
REVERT: A  220 LYS cc_start: 0.7995 (mttt) cc_final: 0.7666 (mmtp)
REVERT: A  261 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7445 (ttp80)
REVERT: A  291 ARG cc_start: 0.7667 (ttp-170) cc_final: 0.7461 (ttp-170)
REVERT: A  342 TYR cc_start: 0.8194 (m-80) cc_final: 0.7772 (m-80)
REVERT: A  355 GLU cc_start: 0.7925 (tp30) cc_final: 0.7613 (tt0)
REVERT: B    1 MET cc_start: 0.5700 (OUTLIER) cc_final: 0.5441 (mmm)
REVERT: B  103 LYS cc_start: 0.8341 (tppp) cc_final: 0.8094 (ttmm)
REVERT: B  118 SER cc_start: 0.8299 (t) cc_final: 0.8069 (p)
REVERT: B  135 ASN cc_start: 0.8424 (m110) cc_final: 0.8170 (m110)
REVERT: B  311 ASP cc_start: 0.7906 (m-30) cc_final: 0.7615 (m-30)
REVERT: B  312 MET cc_start: 0.7222 (mmm) cc_final: 0.6524 (mmt)
REVERT: B  323 MET cc_start: 0.6083 (ptm) cc_final: 0.5863 (ptm)
  outliers start: 27
  outliers final: 7
  residues processed: 212
  average time/residue: 1.4252
  time to fit residues: 321.1914
Evaluate side-chains
  185 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 176
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  246 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 50 optimal weight:   10.0000
   chunk 63 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 27 optimal weight:    5.9990
   chunk 48 optimal weight:    9.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A  87 ASN
A  93 GLN
A 106 GLN
A 131 ASN
A 155 GLN
A 186 GLN
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 347 GLN
B  77 HIS
B 252 ASN
B 256 GLN
B 302 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.138635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.109725 restraints weight = 14914.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.98
r_work: 0.3243 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          1.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  10001  Z= 0.193
  Angle     :  0.620   8.218  14149  Z= 0.329
  Chirality :  0.041   0.169   1628
  Planarity :  0.005   0.058   1293
  Dihedral  : 21.504  84.829   2931
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 24.49 %
    Favored  : 69.57 %
  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:  0.94 (0.29), residues: 797
  helix:  2.16 (0.25), residues: 379
  sheet: -0.15 (0.39), residues: 154
  loop : -1.20 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  45 
 HIS   0.011   0.002   HIS A 278 
 PHE   0.009   0.002   PHE B 236 
 TYR   0.043   0.002   TYR B 233 
 ARG   0.016   0.001   ARG A 266 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04606 (  462)
  hydrogen bonds       : angle       3.78933 ( 1238)
  metal coordination   : bond        0.00885 (    4)
  metal coordination   : angle       4.74109 (    6)
  covalent geometry    : bond        0.00423 ( 9997)
  covalent geometry    : angle       0.61189 (14143)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 208
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASP cc_start: 0.8214 (t0) cc_final: 0.7925 (t0)
REVERT: A   54 ASP cc_start: 0.8373 (m-30) cc_final: 0.8152 (m-30)
REVERT: A  108 GLU cc_start: 0.8622 (mp0) cc_final: 0.8390 (mp0)
REVERT: A  120 LYS cc_start: 0.8301 (pttt) cc_final: 0.8063 (pttt)
REVERT: A  136 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7949 (ttt90)
REVERT: A  137 MET cc_start: 0.8289 (mmm) cc_final: 0.7969 (mmm)
REVERT: A  161 ARG cc_start: 0.8035 (mmt90) cc_final: 0.7759 (mtp85)
REVERT: A  182 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8691 (p)
REVERT: A  197 ARG cc_start: 0.8908 (tmt90) cc_final: 0.8655 (ttp-170)
REVERT: A  246 GLU cc_start: 0.8031 (mp0) cc_final: 0.7797 (mp0)
REVERT: A  261 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7975 (ttp80)
REVERT: A  262 ILE cc_start: 0.8693 (mt) cc_final: 0.8483 (mm)
REVERT: A  266 ARG cc_start: 0.7689 (mtt180) cc_final: 0.7471 (mtt180)
REVERT: A  283 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8025 (mmp80)
REVERT: A  288 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7412 (tm-30)
REVERT: A  291 ARG cc_start: 0.8012 (ttp-170) cc_final: 0.7786 (ttp-170)
REVERT: A  347 GLN cc_start: 0.8549 (tp40) cc_final: 0.8308 (tp40)
REVERT: A  351 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.7227 (t80)
REVERT: B  103 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8329 (ttmm)
REVERT: B  118 SER cc_start: 0.8736 (t) cc_final: 0.8424 (p)
REVERT: B  120 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8555 (tppp)
REVERT: B  135 ASN cc_start: 0.8600 (m110) cc_final: 0.8328 (m110)
REVERT: B  157 MET cc_start: 0.8584 (mpp) cc_final: 0.7909 (mpp)
REVERT: B  233 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7901 (m-80)
REVERT: B  249 GLU cc_start: 0.7344 (tp30) cc_final: 0.7028 (tp30)
REVERT: B  323 MET cc_start: 0.7044 (ptm) cc_final: 0.6572 (ptm)
REVERT: B  346 GLN cc_start: 0.7989 (tt0) cc_final: 0.7183 (mm110)
  outliers start: 41
  outliers final: 12
  residues processed: 224
  average time/residue: 1.4000
  time to fit residues: 331.9220
Evaluate side-chains
  212 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 193
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  136 ARG
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  283 ARG
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  103 LYS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain B residue  310 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 80 optimal weight:    1.9990
   chunk 46 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
A 106 GLN
A 186 GLN
A 256 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.139287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.110535 restraints weight = 14809.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 1.98
r_work: 0.3253 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          1.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10001  Z= 0.131
  Angle     :  0.547   8.966  14149  Z= 0.292
  Chirality :  0.039   0.174   1628
  Planarity :  0.004   0.053   1293
  Dihedral  : 21.474  84.126   2931
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 28.84 %
    Favored  : 67.54 %
  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:  1.33 (0.29), residues: 797
  helix:  2.51 (0.26), residues: 378
  sheet: -0.06 (0.40), residues: 155
  loop : -0.96 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  45 
 HIS   0.006   0.001   HIS A 278 
 PHE   0.015   0.001   PHE A 236 
 TYR   0.017   0.001   TYR B   7 
 ARG   0.009   0.001   ARG A 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04122 (  462)
  hydrogen bonds       : angle       3.57862 ( 1238)
  metal coordination   : bond        0.00652 (    4)
  metal coordination   : angle       4.44406 (    6)
  covalent geometry    : bond        0.00286 ( 9997)
  covalent geometry    : angle       0.53962 (14143)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 201
  time to evaluate  : 1.513 
Fit side-chains
REVERT: A   14 ASP cc_start: 0.8283 (t0) cc_final: 0.8001 (t0)
REVERT: A   50 SER cc_start: 0.8242 (m) cc_final: 0.7960 (t)
REVERT: A  121 ARG cc_start: 0.7884 (ptm-80) cc_final: 0.7651 (ttp80)
REVERT: A  130 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7800 (tm-30)
REVERT: A  136 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7970 (ttt90)
REVERT: A  137 MET cc_start: 0.8303 (mmm) cc_final: 0.7980 (mmm)
REVERT: A  161 ARG cc_start: 0.8022 (mmt90) cc_final: 0.7747 (mtp85)
REVERT: A  178 ASP cc_start: 0.8664 (m-30) cc_final: 0.8363 (m-30)
REVERT: A  197 ARG cc_start: 0.8884 (tmt90) cc_final: 0.8620 (ttp-170)
REVERT: A  220 LYS cc_start: 0.8292 (mttt) cc_final: 0.8091 (mttp)
REVERT: A  261 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8033 (ttp80)
REVERT: A  262 ILE cc_start: 0.8628 (mt) cc_final: 0.8379 (mm)
REVERT: A  288 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7607 (tm-30)
REVERT: A  291 ARG cc_start: 0.7982 (ttp-170) cc_final: 0.7778 (ttp-170)
REVERT: A  323 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8357 (ptp)
REVERT: A  347 GLN cc_start: 0.8580 (tp40) cc_final: 0.8368 (tp40)
REVERT: A  420 SER cc_start: 0.7892 (m) cc_final: 0.7626 (p)
REVERT: B    9 ILE cc_start: 0.8044 (pt) cc_final: 0.7573 (mt)
REVERT: B   22 THR cc_start: 0.8808 (m) cc_final: 0.8324 (p)
REVERT: B  103 LYS cc_start: 0.8430 (tppp) cc_final: 0.8229 (ttmm)
REVERT: B  118 SER cc_start: 0.8649 (t) cc_final: 0.8321 (p)
REVERT: B  120 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8598 (tppp)
REVERT: B  135 ASN cc_start: 0.8555 (m110) cc_final: 0.8346 (m110)
REVERT: B  233 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7578 (m-80)
REVERT: B  249 GLU cc_start: 0.7255 (tp30) cc_final: 0.6954 (tp30)
REVERT: B  262 ILE cc_start: 0.8608 (tt) cc_final: 0.8343 (tp)
REVERT: B  346 GLN cc_start: 0.8055 (tt0) cc_final: 0.7333 (mm-40)
  outliers start: 25
  outliers final: 10
  residues processed: 216
  average time/residue: 1.9422
  time to fit residues: 444.8969
Evaluate side-chains
  204 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 190
  time to evaluate  : 1.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  136 ARG
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  318 CYS
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain B residue  310 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 70 optimal weight:    4.9990
   chunk 77 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  26 GLN
A  93 GLN
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 GLN
B  72 HIS
B 256 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.132811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.104150 restraints weight = 14744.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.95
r_work: 0.3148 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          1.3082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  10001  Z= 0.242
  Angle     :  0.650  10.829  14149  Z= 0.340
  Chirality :  0.042   0.166   1628
  Planarity :  0.005   0.062   1293
  Dihedral  : 21.496  83.180   2931
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 27.83 %
    Favored  : 66.23 %
  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:  0.93 (0.29), residues: 797
  helix:  2.15 (0.26), residues: 379
  sheet: -0.19 (0.39), residues: 159
  loop : -1.20 (0.35), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  45 
 HIS   0.009   0.002   HIS A 278 
 PHE   0.012   0.002   PHE A 253 
 TYR   0.021   0.002   TYR B   7 
 ARG   0.010   0.001   ARG A 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04986 (  462)
  hydrogen bonds       : angle       3.79618 ( 1238)
  metal coordination   : bond        0.01042 (    4)
  metal coordination   : angle       5.64888 (    6)
  covalent geometry    : bond        0.00539 ( 9997)
  covalent geometry    : angle       0.64004 (14143)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 195
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7726 (tm-30)
REVERT: A  136 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8125 (ttm-80)
REVERT: A  137 MET cc_start: 0.8581 (mmm) cc_final: 0.8205 (mmm)
REVERT: A  141 ASP cc_start: 0.8368 (p0) cc_final: 0.8129 (p0)
REVERT: A  161 ARG cc_start: 0.8157 (mmt90) cc_final: 0.7888 (mtp85)
REVERT: A  261 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8094 (ttp80)
REVERT: A  270 TYR cc_start: 0.8658 (p90) cc_final: 0.8204 (p90)
REVERT: A  288 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7510 (tm-30)
REVERT: A  291 ARG cc_start: 0.7993 (ttp-170) cc_final: 0.7755 (ttp-170)
REVERT: A  292 ASP cc_start: 0.8416 (t0) cc_final: 0.8174 (m-30)
REVERT: A  347 GLN cc_start: 0.8572 (tp40) cc_final: 0.8369 (tp40)
REVERT: A  351 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.7136 (t80)
REVERT: A  406 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7682 (ttp80)
REVERT: A  420 SER cc_start: 0.7928 (m) cc_final: 0.7618 (p)
REVERT: B   22 THR cc_start: 0.8905 (m) cc_final: 0.8614 (p)
REVERT: B   46 MET cc_start: 0.8942 (tpp) cc_final: 0.8654 (mmt)
REVERT: B  118 SER cc_start: 0.8851 (t) cc_final: 0.8542 (p)
REVERT: B  120 LYS cc_start: 0.8960 (mmmm) cc_final: 0.8654 (tppp)
REVERT: B  135 ASN cc_start: 0.8425 (m110) cc_final: 0.8201 (m-40)
REVERT: B  155 GLN cc_start: 0.8111 (tp-100) cc_final: 0.7825 (tp-100)
REVERT: B  157 MET cc_start: 0.8636 (mpp) cc_final: 0.8189 (mpp)
REVERT: B  178 ASP cc_start: 0.7854 (m-30) cc_final: 0.7466 (m-30)
REVERT: B  199 ASN cc_start: 0.8593 (t0) cc_final: 0.8344 (m110)
REVERT: B  200 LYS cc_start: 0.8193 (mmmt) cc_final: 0.7932 (mmmt)
REVERT: B  233 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7479 (t80)
REVERT: B  243 TYR cc_start: 0.8088 (m-80) cc_final: 0.7735 (m-80)
REVERT: B  249 GLU cc_start: 0.7190 (tp30) cc_final: 0.6880 (tp30)
REVERT: B  262 ILE cc_start: 0.8759 (tt) cc_final: 0.8539 (tt)
REVERT: B  315 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8065 (tttt)
REVERT: B  371 ARG cc_start: 0.6863 (ttt90) cc_final: 0.6414 (ttt-90)
REVERT: B  414 ASP cc_start: 0.7476 (m-30) cc_final: 0.7257 (m-30)
REVERT: B  416 ILE cc_start: 0.8004 (pp) cc_final: 0.7782 (mt)
  outliers start: 41
  outliers final: 16
  residues processed: 220
  average time/residue: 1.5342
  time to fit residues: 355.8665
Evaluate side-chains
  209 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 187
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  136 ARG
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  318 CYS
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 LYS
Chi-restraints excluded: chain B residue  324 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 78 optimal weight:    8.9990
   chunk 34 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 53 optimal weight:    8.9990
   chunk 33 optimal weight:    8.9990
   chunk 47 optimal weight:   10.0000
   chunk 66 optimal weight:    0.3980
   chunk 25 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
A 139 HIS
A 186 GLN
A 237 GLN
A 366 GLN
A 377 ASN
** B  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.130223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.101676 restraints weight = 14800.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 1.91
r_work: 0.3165 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          1.3371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10001  Z= 0.183
  Angle     :  0.606   9.908  14149  Z= 0.320
  Chirality :  0.040   0.160   1628
  Planarity :  0.005   0.064   1293
  Dihedral  : 21.495  81.465   2931
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 32.17 %
    Favored  : 63.62 %
  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:  1.16 (0.29), residues: 797
  helix:  2.35 (0.26), residues: 379
  sheet: -0.11 (0.40), residues: 161
  loop : -1.07 (0.35), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  45 
 HIS   0.005   0.001   HIS B  72 
 PHE   0.010   0.002   PHE A 253 
 TYR   0.019   0.002   TYR B 351 
 ARG   0.015   0.001   ARG A 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04478 (  462)
  hydrogen bonds       : angle       3.66778 ( 1238)
  metal coordination   : bond        0.00881 (    4)
  metal coordination   : angle       5.17343 (    6)
  covalent geometry    : bond        0.00407 ( 9997)
  covalent geometry    : angle       0.59712 (14143)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 198
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7702 (tm-30)
REVERT: A  136 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7742 (ttt90)
REVERT: A  137 MET cc_start: 0.8630 (mmm) cc_final: 0.8259 (mmm)
REVERT: A  141 ASP cc_start: 0.8390 (p0) cc_final: 0.8189 (p0)
REVERT: A  155 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8345 (mm-40)
REVERT: A  161 ARG cc_start: 0.8130 (mmt90) cc_final: 0.7845 (mtp85)
REVERT: A  261 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8042 (ttp80)
REVERT: A  283 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8059 (mmp80)
REVERT: A  288 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7721 (tm-30)
REVERT: A  292 ASP cc_start: 0.8415 (t0) cc_final: 0.8147 (m-30)
REVERT: A  346 GLN cc_start: 0.8720 (mt0) cc_final: 0.8475 (mt0)
REVERT: A  347 GLN cc_start: 0.8524 (tp40) cc_final: 0.8319 (tp40)
REVERT: A  351 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.7138 (t80)
REVERT: A  420 SER cc_start: 0.7922 (m) cc_final: 0.7646 (p)
REVERT: B   22 THR cc_start: 0.8841 (m) cc_final: 0.8571 (p)
REVERT: B   31 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8094 (p)
REVERT: B  118 SER cc_start: 0.8766 (t) cc_final: 0.8464 (p)
REVERT: B  155 GLN cc_start: 0.8262 (tp-100) cc_final: 0.7996 (tp-100)
REVERT: B  157 MET cc_start: 0.8620 (mpp) cc_final: 0.8261 (mpp)
REVERT: B  178 ASP cc_start: 0.7843 (m-30) cc_final: 0.7478 (m-30)
REVERT: B  200 LYS cc_start: 0.8210 (mmmt) cc_final: 0.7901 (mmmt)
REVERT: B  233 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7425 (t80)
REVERT: B  249 GLU cc_start: 0.7142 (tp30) cc_final: 0.6826 (tp30)
  outliers start: 29
  outliers final: 13
  residues processed: 216
  average time/residue: 1.4665
  time to fit residues: 334.4266
Evaluate side-chains
  211 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 192
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  136 ARG
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  283 ARG
Chi-restraints excluded: chain A residue  318 CYS
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  246 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 51 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
A 139 HIS
B  36 ASN
** B  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.130617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.102189 restraints weight = 14865.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.90
r_work: 0.3166 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          1.3581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10001  Z= 0.171
  Angle     :  0.596   9.077  14149  Z= 0.317
  Chirality :  0.039   0.155   1628
  Planarity :  0.005   0.071   1293
  Dihedral  : 21.533  81.376   2931
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 33.91 %
    Favored  : 61.88 %
  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:  1.27 (0.29), residues: 797
  helix:  2.43 (0.26), residues: 379
  sheet: -0.09 (0.39), residues: 161
  loop : -0.97 (0.35), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  45 
 HIS   0.004   0.001   HIS A 278 
 PHE   0.009   0.001   PHE A 253 
 TYR   0.015   0.001   TYR B   7 
 ARG   0.018   0.001   ARG A 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04348 (  462)
  hydrogen bonds       : angle       3.67163 ( 1238)
  metal coordination   : bond        0.01101 (    4)
  metal coordination   : angle       5.02930 (    6)
  covalent geometry    : bond        0.00380 ( 9997)
  covalent geometry    : angle       0.58696 (14143)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 206
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 SER cc_start: 0.8195 (OUTLIER) cc_final: 0.7967 (t)
REVERT: A  130 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7688 (tm-30)
REVERT: A  137 MET cc_start: 0.8642 (mmm) cc_final: 0.8287 (mmm)
REVERT: A  155 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8352 (mm-40)
REVERT: A  210 GLU cc_start: 0.8040 (mp0) cc_final: 0.7408 (mp0)
REVERT: A  261 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8060 (ttp80)
REVERT: A  270 TYR cc_start: 0.8442 (p90) cc_final: 0.7599 (p90)
REVERT: A  283 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8053 (mmp80)
REVERT: A  291 ARG cc_start: 0.7981 (ttp-170) cc_final: 0.7711 (tpp80)
REVERT: A  346 GLN cc_start: 0.8722 (mt0) cc_final: 0.8468 (mt0)
REVERT: A  351 TYR cc_start: 0.7412 (OUTLIER) cc_final: 0.7071 (t80)
REVERT: A  420 SER cc_start: 0.7939 (m) cc_final: 0.7646 (p)
REVERT: B   22 THR cc_start: 0.8872 (m) cc_final: 0.8625 (p)
REVERT: B   31 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8030 (p)
REVERT: B   46 MET cc_start: 0.8843 (tpp) cc_final: 0.8612 (mmt)
REVERT: B  118 SER cc_start: 0.8749 (t) cc_final: 0.8457 (p)
REVERT: B  157 MET cc_start: 0.8606 (mpp) cc_final: 0.8276 (mpp)
REVERT: B  177 MET cc_start: 0.8209 (mmp) cc_final: 0.7914 (mmp)
REVERT: B  178 ASP cc_start: 0.7864 (m-30) cc_final: 0.7422 (m-30)
REVERT: B  179 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7875 (ptp-170)
REVERT: B  233 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7412 (t80)
REVERT: B  249 GLU cc_start: 0.7120 (tp30) cc_final: 0.6794 (tp30)
REVERT: B  315 LYS cc_start: 0.8497 (tttt) cc_final: 0.8024 (tttm)
REVERT: B  362 LYS cc_start: 0.8672 (mmmm) cc_final: 0.8251 (mmmm)
  outliers start: 29
  outliers final: 17
  residues processed: 224
  average time/residue: 1.6752
  time to fit residues: 396.0260
Evaluate side-chains
  222 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 198
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  283 ARG
Chi-restraints excluded: chain A residue  318 CYS
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  133 SER
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  179 ARG
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  246 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 35 optimal weight:    0.5980
   chunk 62 optimal weight:    4.9990
   chunk 59 optimal weight:    7.9990
   chunk 34 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 37 optimal weight:    9.9990
   chunk 81 optimal weight:    7.9990
   chunk 47 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
A 139 HIS
A 366 GLN
A 377 ASN
** B  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.128553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.100491 restraints weight = 14515.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 1.87
r_work: 0.3138 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          1.3842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  10001  Z= 0.223
  Angle     :  0.641  10.363  14149  Z= 0.338
  Chirality :  0.042   0.177   1628
  Planarity :  0.005   0.085   1293
  Dihedral  : 21.583  83.823   2931
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 35.07 %
    Favored  : 60.72 %
  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:  1.16 (0.29), residues: 797
  helix:  2.31 (0.26), residues: 379
  sheet: -0.06 (0.39), residues: 161
  loop : -1.03 (0.35), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  45 
 HIS   0.005   0.001   HIS A 278 
 PHE   0.010   0.002   PHE A 253 
 TYR   0.013   0.002   TYR B 185 
 ARG   0.019   0.001   ARG A 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04732 (  462)
  hydrogen bonds       : angle       3.76211 ( 1238)
  metal coordination   : bond        0.00962 (    4)
  metal coordination   : angle       5.39159 (    6)
  covalent geometry    : bond        0.00498 ( 9997)
  covalent geometry    : angle       0.63134 (14143)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 198
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 SER cc_start: 0.8199 (OUTLIER) cc_final: 0.7998 (t)
REVERT: A  130 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7670 (tm-30)
REVERT: A  137 MET cc_start: 0.8602 (mmm) cc_final: 0.8293 (mmm)
REVERT: A  141 ASP cc_start: 0.8255 (p0) cc_final: 0.8035 (p0)
REVERT: A  155 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8394 (mm-40)
REVERT: A  228 VAL cc_start: 0.8688 (m) cc_final: 0.8473 (p)
REVERT: A  269 LYS cc_start: 0.8627 (pttt) cc_final: 0.8356 (pttt)
REVERT: A  291 ARG cc_start: 0.7975 (ttp-170) cc_final: 0.7756 (tpp80)
REVERT: A  351 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.7045 (t80)
REVERT: A  355 GLU cc_start: 0.8279 (tp30) cc_final: 0.7877 (tp30)
REVERT: A  420 SER cc_start: 0.7902 (m) cc_final: 0.7615 (p)
REVERT: B    6 ARG cc_start: 0.8191 (ttm110) cc_final: 0.7669 (ttm110)
REVERT: B   22 THR cc_start: 0.8871 (m) cc_final: 0.8638 (p)
REVERT: B   31 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.7994 (p)
REVERT: B  118 SER cc_start: 0.8787 (t) cc_final: 0.8494 (p)
REVERT: B  157 MET cc_start: 0.8662 (mpp) cc_final: 0.8391 (mpp)
REVERT: B  177 MET cc_start: 0.8227 (mmp) cc_final: 0.7881 (tpp)
REVERT: B  178 ASP cc_start: 0.7918 (m-30) cc_final: 0.7528 (m-30)
REVERT: B  179 ARG cc_start: 0.8137 (ptp-170) cc_final: 0.7922 (ptp-170)
REVERT: B  200 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7619 (mmmt)
REVERT: B  214 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6814 (ptp-110)
REVERT: B  233 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7487 (t80)
REVERT: B  289 GLN cc_start: 0.7570 (tp40) cc_final: 0.7272 (tp40)
REVERT: B  315 LYS cc_start: 0.8522 (tttt) cc_final: 0.8016 (tttm)
REVERT: B  335 ARG cc_start: 0.7668 (mtt-85) cc_final: 0.7293 (mtt-85)
REVERT: B  349 ILE cc_start: 0.7503 (mm) cc_final: 0.7022 (tt)
  outliers start: 29
  outliers final: 15
  residues processed: 211
  average time/residue: 1.7758
  time to fit residues: 395.8187
Evaluate side-chains
  215 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 195
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  283 ARG
Chi-restraints excluded: chain A residue  318 CYS
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  246 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 47 optimal weight:   10.0000
   chunk 35 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   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  93 GLN
A 139 HIS
A 256 GLN
A 366 GLN
B  70 ASN
** B  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 403 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.131453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.103406 restraints weight = 14914.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 1.91
r_work: 0.3182 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          1.3932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10001  Z= 0.144
  Angle     :  0.616   8.975  14149  Z= 0.326
  Chirality :  0.040   0.387   1628
  Planarity :  0.005   0.081   1293
  Dihedral  : 21.562  80.496   2931
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 36.52 %
    Favored  : 60.14 %
  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:  1.36 (0.30), residues: 797
  helix:  2.50 (0.26), residues: 374
  sheet: -0.03 (0.39), residues: 161
  loop : -0.85 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  45 
 HIS   0.004   0.001   HIS A 278 
 PHE   0.009   0.001   PHE A 253 
 TYR   0.012   0.001   TYR B   7 
 ARG   0.020   0.001   ARG A 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04163 (  462)
  hydrogen bonds       : angle       3.71276 ( 1238)
  metal coordination   : bond        0.00579 (    4)
  metal coordination   : angle       4.56372 (    6)
  covalent geometry    : bond        0.00322 ( 9997)
  covalent geometry    : angle       0.60878 (14143)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 199
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8332 (m-30)
REVERT: A  130 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7711 (tm-30)
REVERT: A  137 MET cc_start: 0.8630 (mmm) cc_final: 0.8311 (mmm)
REVERT: A  155 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8394 (mm-40)
REVERT: A  161 ARG cc_start: 0.8241 (mmt90) cc_final: 0.7850 (mtp85)
REVERT: A  228 VAL cc_start: 0.8629 (m) cc_final: 0.8400 (p)
REVERT: A  269 LYS cc_start: 0.8572 (pttt) cc_final: 0.8345 (pttp)
REVERT: A  283 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8062 (mmp80)
REVERT: A  351 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.6980 (t80)
REVERT: A  410 ILE cc_start: 0.8054 (mm) cc_final: 0.7800 (mp)
REVERT: A  420 SER cc_start: 0.7871 (m) cc_final: 0.7602 (p)
REVERT: B    6 ARG cc_start: 0.8270 (ttm110) cc_final: 0.7679 (ttm110)
REVERT: B   22 THR cc_start: 0.8848 (m) cc_final: 0.8629 (p)
REVERT: B   31 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.7920 (p)
REVERT: B  114 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8486 (ptp)
REVERT: B  118 SER cc_start: 0.8695 (t) cc_final: 0.8396 (p)
REVERT: B  157 MET cc_start: 0.8641 (mpp) cc_final: 0.8423 (mpp)
REVERT: B  178 ASP cc_start: 0.7901 (m-30) cc_final: 0.7571 (m-30)
REVERT: B  179 ARG cc_start: 0.8162 (ptp-170) cc_final: 0.7946 (ptp-170)
REVERT: B  200 LYS cc_start: 0.8265 (mmmt) cc_final: 0.7636 (mmmt)
REVERT: B  214 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6758 (ptp-110)
REVERT: B  233 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7454 (t80)
REVERT: B  289 GLN cc_start: 0.7579 (tp40) cc_final: 0.7279 (tp40)
REVERT: B  315 LYS cc_start: 0.8423 (tttt) cc_final: 0.8208 (tttm)
REVERT: B  316 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7263 (mm-30)
REVERT: B  335 ARG cc_start: 0.7594 (mtt-85) cc_final: 0.7245 (mtt-85)
REVERT: B  349 ILE cc_start: 0.7381 (mm) cc_final: 0.6947 (tt)
  outliers start: 23
  outliers final: 6
  residues processed: 212
  average time/residue: 1.6683
  time to fit residues: 372.6042
Evaluate side-chains
  206 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 193
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  283 ARG
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  246 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 69 optimal weight:    0.0770
   chunk 60 optimal weight:    5.9990
   chunk 86 optimal weight:    0.7980
   chunk 37 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   overall best weight:    1.9744

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
A 139 HIS
A 186 GLN
A 366 GLN
A 377 ASN
B  70 ASN
** B  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.130460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.102292 restraints weight = 14744.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.89
r_work: 0.3161 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          1.4035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10001  Z= 0.175
  Angle     :  0.631   8.912  14149  Z= 0.333
  Chirality :  0.040   0.164   1628
  Planarity :  0.005   0.084   1293
  Dihedral  : 21.554  81.997   2931
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 37.39 %
    Favored  : 60.43 %
  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:  1.34 (0.29), residues: 797
  helix:  2.45 (0.26), residues: 374
  sheet: -0.04 (0.39), residues: 160
  loop : -0.80 (0.36), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  45 
 HIS   0.004   0.001   HIS A 278 
 PHE   0.008   0.001   PHE A 336 
 TYR   0.020   0.002   TYR B   7 
 ARG   0.020   0.001   ARG A 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04283 (  462)
  hydrogen bonds       : angle       3.72576 ( 1238)
  metal coordination   : bond        0.00711 (    4)
  metal coordination   : angle       4.81290 (    6)
  covalent geometry    : bond        0.00392 ( 9997)
  covalent geometry    : angle       0.62305 (14143)

===============================================================================
Job complete
usr+sys time: 9107.23 seconds
wall clock time: 158 minutes 51.95 seconds (9531.95 seconds total)