Starting phenix.real_space_refine
on Sat May 10 12:41:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sv1_40781/05_2025/8sv1_40781.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sv1_40781/05_2025/8sv1_40781.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sv1_40781/05_2025/8sv1_40781.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sv1_40781/05_2025/8sv1_40781.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sv1_40781/05_2025/8sv1_40781.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sv1_40781/05_2025/8sv1_40781.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.068
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: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    4004      2.51       5
     N    1062      2.21       5
     O    1210      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6330
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1158
          Classifications: {'peptide': 148}
          Link IDs: {'PTRANS': 7, 'TRANS': 140}
    Chain: "B"
      Number of atoms: 718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 718
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 5, 'TRANS': 82}
    Chain: "a"
      Number of atoms: 1158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1158
          Classifications: {'peptide': 148}
          Link IDs: {'PTRANS': 7, 'TRANS': 140}
    Chain: "b"
      Number of atoms: 718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 718
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 5, 'TRANS': 82}
    Chain: "C"
      Number of atoms: 1289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 1289
          Classifications: {'peptide': 160}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 155}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "c"
      Number of atoms: 1289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 1289
          Classifications: {'peptide': 160}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 155}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 4.64, per 1000 atoms: 0.73
  Number of scatterers: 6330
  At special positions: 0
  Unit cell: (72.21, 135.29, 65.57, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1210      8.00
     N    1062      7.00
     C    4004      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: 1.53
  Conformation dependent library (CDL) restraints added in 976.0 milliseconds
  

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 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:
      14 helices and 12 sheets defined
      19.7% alpha, 21.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 181 through 197
    Processing helix  chain 'A' and resid 207 through 221
    Processing helix  chain 'A' and resid 222 through 227
    Processing helix  chain 'A' and resid 257 through 265
      removed outlier: 3.517A  pdb=" N   LEU A 265 " --> pdb=" O   ILE A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 274
      removed outlier: 3.751A  pdb=" N   LYS A 274 " --> pdb=" O   PRO A 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 361
    Processing helix  chain 'B' and resid 365 through 376
    Processing helix  chain 'a' and resid 181 through 197
    Processing helix  chain 'a' and resid 207 through 221
    Processing helix  chain 'a' and resid 223 through 227
    Processing helix  chain 'a' and resid 257 through 264
    Processing helix  chain 'a' and resid 270 through 274
      removed outlier: 3.558A  pdb=" N   LYS a 274 " --> pdb=" O   PRO a 271 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 347 through 361
      removed outlier: 3.573A  pdb=" N   ALA b 361 " --> pdb=" O   MET b 357 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 365 through 376
    Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 204
      removed outlier: 3.554A  pdb=" N   LEU A 232 " --> pdb=" O   VAL A 279 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   LYS A 278 " --> pdb=" O   ILE B 328 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 238 through 239
    Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 296
      removed outlier: 3.863A  pdb=" N   PHE A 295 " --> pdb=" O   LYS b 319 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LYS b 319 " --> pdb=" O   PHE A 295 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 320 through 322
    Processing sheet with id=AA5, first strand: chain 'B' and resid 340 through 341
    Processing sheet with id=AA6, first strand: chain 'a' and resid 199 through 204
      removed outlier: 3.516A  pdb=" N   ALA a 165 " --> pdb=" O   SER a 199 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   PHE a 231 " --> pdb=" O   LEU a 164 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU a 232 " --> pdb=" O   VAL a 279 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'a' and resid 243 through 244
    Processing sheet with id=AA8, first strand: chain 'b' and resid 340 through 341
    Processing sheet with id=AA9, first strand: chain 'C' and resid 24 through 25
      removed outlier: 3.721A  pdb=" N   ALA C 162 " --> pdb=" O   ILE C 173 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   LEU C 161 " --> pdb=" O   PHE C 187 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   PHE C 187 " --> pdb=" O   LEU C 161 " (cutoff:3.500A)
      removed outlier: 18.414A  pdb=" N   ILE C 185 " --> pdb=" O   SER C 153 " (cutoff:3.500A)
      removed outlier: 13.593A  pdb=" N   SER C 153 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   PHE C 187 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   PHE C 151 " --> pdb=" O   PHE C 187 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL C 189 " --> pdb=" O   MET C 149 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   MET C 149 " --> pdb=" O   VAL C 189 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ALA C  97 " --> pdb=" O   TYR C  88 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 46
      removed outlier: 5.857A  pdb=" N   SER C  46 " --> pdb=" O   THR C 188 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   GLN C 190 " --> pdb=" O   SER C  46 " (cutoff:3.500A)
      removed outlier: 18.414A  pdb=" N   ILE C 185 " --> pdb=" O   SER C 153 " (cutoff:3.500A)
      removed outlier: 13.593A  pdb=" N   SER C 153 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   PHE C 187 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   PHE C 151 " --> pdb=" O   PHE C 187 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL C 189 " --> pdb=" O   MET C 149 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   MET C 149 " --> pdb=" O   VAL C 189 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   ILE C 100 " --> pdb=" O   LEU C 110 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU C 110 " --> pdb=" O   ILE C 100 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'c' and resid 24 through 25
      removed outlier: 3.721A  pdb=" N   ALA c 162 " --> pdb=" O   ILE c 173 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   LEU c 161 " --> pdb=" O   PHE c 187 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   PHE c 187 " --> pdb=" O   LEU c 161 " (cutoff:3.500A)
      removed outlier: 18.414A  pdb=" N   ILE c 185 " --> pdb=" O   SER c 153 " (cutoff:3.500A)
      removed outlier: 13.592A  pdb=" N   SER c 153 " --> pdb=" O   ILE c 185 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   PHE c 187 " --> pdb=" O   PHE c 151 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   PHE c 151 " --> pdb=" O   PHE c 187 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL c 189 " --> pdb=" O   MET c 149 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   MET c 149 " --> pdb=" O   VAL c 189 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ALA c  97 " --> pdb=" O   TYR c  88 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'c' and resid 45 through 46
      removed outlier: 5.856A  pdb=" N   SER c  46 " --> pdb=" O   THR c 188 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   GLN c 190 " --> pdb=" O   SER c  46 " (cutoff:3.500A)
      removed outlier: 18.414A  pdb=" N   ILE c 185 " --> pdb=" O   SER c 153 " (cutoff:3.500A)
      removed outlier: 13.592A  pdb=" N   SER c 153 " --> pdb=" O   ILE c 185 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   PHE c 187 " --> pdb=" O   PHE c 151 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   PHE c 151 " --> pdb=" O   PHE c 187 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL c 189 " --> pdb=" O   MET c 149 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   MET c 149 " --> pdb=" O   VAL c 189 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   ILE c 100 " --> pdb=" O   LEU c 110 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU c 110 " --> pdb=" O   ILE c 100 " (cutoff:3.500A)

    199 hydrogen bonds defined for protein.
    519 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.81

  Time building geometry restraints manager: 1.81 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1983
        1.33 -     1.46: 1005
        1.46 -     1.58: 3378
        1.58 -     1.70: 0
        1.70 -     1.82: 84
  Bond restraints: 6450
  Sorted by residual:
  bond pdb=" N   PHE C  83 "
       pdb=" CA  PHE C  83 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.036 1.29e-02 6.01e+03 7.84e+00
  bond pdb=" N   PHE c  83 "
       pdb=" CA  PHE c  83 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.29e-02 6.01e+03 7.62e+00
  bond pdb=" N   MET C 122 "
       pdb=" CA  MET C 122 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.031 1.29e-02 6.01e+03 5.89e+00
  bond pdb=" N   MET c 122 "
       pdb=" CA  MET c 122 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.29e-02 6.01e+03 5.42e+00
  bond pdb=" C   ARG a 221 "
       pdb=" N   PRO a 222 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.018 9.40e-03 1.13e+04 3.67e+00
  ... (remaining 6445 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.47: 8629
        3.47 -     6.94: 44
        6.94 -    10.42: 7
       10.42 -    13.89: 0
       13.89 -    17.36: 2
  Bond angle restraints: 8682
  Sorted by residual:
  angle pdb=" N   ILE c  84 "
        pdb=" CA  ILE c  84 "
        pdb=" C   ILE c  84 "
      ideal   model   delta    sigma   weight residual
     109.30  125.39  -16.09 1.25e+00 6.40e-01 1.66e+02
  angle pdb=" N   ILE C  84 "
        pdb=" CA  ILE C  84 "
        pdb=" C   ILE C  84 "
      ideal   model   delta    sigma   weight residual
     109.37  126.73  -17.36 1.35e+00 5.49e-01 1.65e+02
  angle pdb=" N   ILE c  84 "
        pdb=" CA  ILE c  84 "
        pdb=" CB  ILE c  84 "
      ideal   model   delta    sigma   weight residual
     110.31  101.58    8.73 1.23e+00 6.61e-01 5.04e+01
  angle pdb=" N   ILE C  84 "
        pdb=" CA  ILE C  84 "
        pdb=" CB  ILE C  84 "
      ideal   model   delta    sigma   weight residual
     110.13  101.48    8.65 1.34e+00 5.57e-01 4.17e+01
  angle pdb=" CA  ARG b 383 "
        pdb=" C   ARG b 383 "
        pdb=" O   ARG b 383 "
      ideal   model   delta    sigma   weight residual
     122.36  118.10    4.26 1.21e+00 6.83e-01 1.24e+01
  ... (remaining 8677 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.05: 3240
       14.05 -    28.10: 475
       28.10 -    42.14: 187
       42.14 -    56.19: 37
       56.19 -    70.24: 15
  Dihedral angle restraints: 3954
    sinusoidal: 1636
      harmonic: 2318
  Sorted by residual:
  dihedral pdb=" CA  VAL C  47 "
           pdb=" C   VAL C  47 "
           pdb=" N   ILE C  48 "
           pdb=" CA  ILE C  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.06  -20.94     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" CA  VAL c  47 "
           pdb=" C   VAL c  47 "
           pdb=" N   ILE c  48 "
           pdb=" CA  ILE c  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.09  -20.91     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" CA  GLU C 105 "
           pdb=" C   GLU C 105 "
           pdb=" N   LYS C 106 "
           pdb=" CA  LYS C 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.83   17.17     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 3951 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 781
       0.058 -    0.116: 164
       0.116 -    0.175: 17
       0.175 -    0.233: 1
       0.233 -    0.291: 1
  Chirality restraints: 964
  Sorted by residual:
  chirality pdb=" CA  ILE C  84 "
            pdb=" N   ILE C  84 "
            pdb=" C   ILE C  84 "
            pdb=" CB  ILE C  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.14    0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CA  ILE c  84 "
            pdb=" N   ILE c  84 "
            pdb=" C   ILE c  84 "
            pdb=" CB  ILE c  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.21    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CB  ILE B 318 "
            pdb=" CA  ILE B 318 "
            pdb=" CG1 ILE B 318 "
            pdb=" CG2 ILE B 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.17 2.00e-01 2.50e+01 7.38e-01
  ... (remaining 961 not shown)

  Planarity restraints: 1122
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG c  49 "    0.474 9.50e-02 1.11e+02   2.13e-01 2.76e+01
        pdb=" NE  ARG c  49 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG c  49 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG c  49 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG c  49 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  49 "   -0.474 9.50e-02 1.11e+02   2.13e-01 2.76e+01
        pdb=" NE  ARG C  49 "    0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  49 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  49 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  49 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG b 383 "    0.415 9.50e-02 1.11e+02   1.86e-01 2.12e+01
        pdb=" NE  ARG b 383 "   -0.025 2.00e-02 2.50e+03
        pdb=" CZ  ARG b 383 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG b 383 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG b 383 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1119 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 883
        2.76 -     3.29: 6106
        3.29 -     3.83: 10062
        3.83 -     4.36: 11584
        4.36 -     4.90: 20099
  Nonbonded interactions: 48734
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 162 "
            pdb=" OG1 THR A 226 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OG  SER B 332 "
            pdb=" OG  SER B 339 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   THR a 162 "
            pdb=" OG1 THR a 162 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OH  TYR A 198 "
            pdb=" OG  SER A 229 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OE2 GLU b 324 "
            pdb=" NH2 ARG b 391 "
     model   vdw
     2.300 3.120
  ... (remaining 48729 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'a'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'b'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'c'
}

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 group one per residue
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:             0.990
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.390
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
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   0.036   6450  Z= 0.176
  Angle     :  0.755  17.360   8682  Z= 0.439
  Chirality :  0.046   0.291    964
  Planarity :  0.012   0.213   1122
  Dihedral  : 16.023  70.239   2438
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  6.19 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 17.69 %
    Favored  : 81.62 %
  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: -1.32 (0.29), residues: 776
  helix:  1.09 (0.43), residues: 136
  sheet: -0.71 (0.44), residues: 158
  loop : -1.59 (0.26), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP b 340 
 HIS   0.005   0.001   HIS a 224 
 PHE   0.010   0.001   PHE C  18 
 TYR   0.007   0.001   TYR c  88 
 ARG   0.005   0.001   ARG A 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22246 (  187)
  hydrogen bonds       : angle       8.10325 (  519)
  covalent geometry    : bond        0.00337 ( 6450)
  covalent geometry    : angle       0.75463 ( 8682)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 258
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ARG cc_start: 0.7063 (ptt180) cc_final: 0.6776 (ptt180)
REVERT: A  283 GLN cc_start: 0.7597 (tm-30) cc_final: 0.6709 (tm-30)
REVERT: a  225 LYS cc_start: 0.8484 (tttt) cc_final: 0.8251 (mmtp)
REVERT: a  272 SER cc_start: 0.7953 (m) cc_final: 0.7554 (m)
REVERT: a  283 GLN cc_start: 0.7114 (tm-30) cc_final: 0.6670 (tm-30)
REVERT: a  296 LYS cc_start: 0.8569 (tppt) cc_final: 0.7754 (mtpt)
REVERT: C   50 ASN cc_start: 0.7295 (m110) cc_final: 0.7031 (m110)
REVERT: C  164 GLU cc_start: 0.5615 (tp30) cc_final: 0.5142 (tp30)
REVERT: c   50 ASN cc_start: 0.7226 (m110) cc_final: 0.6936 (m110)
REVERT: c  164 GLU cc_start: 0.5408 (tp30) cc_final: 0.5030 (tp30)
  outliers start: 5
  outliers final: 3
  residues processed: 259
  average time/residue: 0.2347
  time to fit residues: 77.0255
Evaluate side-chains
  233 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 230
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue  383 ARG
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain c residue   49 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 44 optimal weight:    4.9990
   chunk 69 optimal weight:    0.2980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 337 ASN
C 147 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.228508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.157174 restraints weight = 6139.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.165631 restraints weight = 2850.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.171004 restraints weight = 1823.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6837
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6450  Z= 0.159
  Angle     :  0.638   8.038   8682  Z= 0.334
  Chirality :  0.046   0.175    964
  Planarity :  0.005   0.056   1122
  Dihedral  :  6.266  59.503    852
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 21.73 %
    Favored  : 75.35 %
  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: -1.35 (0.29), residues: 776
  helix:  0.99 (0.43), residues: 138
  sheet: -0.56 (0.45), residues: 148
  loop : -1.64 (0.25), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP a 294 
 HIS   0.005   0.001   HIS A 224 
 PHE   0.027   0.002   PHE b 370 
 TYR   0.007   0.001   TYR c  88 
 ARG   0.004   0.001   ARG B 352 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03979 (  187)
  hydrogen bonds       : angle       5.51768 (  519)
  covalent geometry    : bond        0.00349 ( 6450)
  covalent geometry    : angle       0.63775 ( 8682)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 220
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 GLN cc_start: 0.7498 (mp10) cc_final: 0.7208 (mp10)
REVERT: A  283 GLN cc_start: 0.7478 (tm-30) cc_final: 0.6430 (tm-30)
REVERT: a  225 LYS cc_start: 0.8992 (tttt) cc_final: 0.8395 (mmtp)
REVERT: a  241 GLU cc_start: 0.8474 (mp0) cc_final: 0.8201 (mp0)
REVERT: a  283 GLN cc_start: 0.7425 (tm-30) cc_final: 0.6318 (tm-30)
REVERT: a  296 LYS cc_start: 0.8463 (tppt) cc_final: 0.7678 (mttt)
REVERT: C   50 ASN cc_start: 0.7019 (m110) cc_final: 0.6678 (m110)
REVERT: C  164 GLU cc_start: 0.5104 (tp30) cc_final: 0.4788 (tp30)
REVERT: c   50 ASN cc_start: 0.6793 (m110) cc_final: 0.6454 (m110)
REVERT: c  176 LYS cc_start: 0.8831 (mmtp) cc_final: 0.8216 (mtmt)
  outliers start: 21
  outliers final: 16
  residues processed: 227
  average time/residue: 0.2014
  time to fit residues: 57.9213
Evaluate side-chains
  227 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 211
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain a residue  249 SER
Chi-restraints excluded: chain b residue  348 VAL
Chi-restraints excluded: chain b residue  383 ARG
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain b residue  393 THR
Chi-restraints excluded: chain C residue   28 GLU
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain c residue   49 ARG
Chi-restraints excluded: chain c residue   82 ILE
Chi-restraints excluded: chain c residue  160 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 68 optimal weight:    9.9990
   chunk 58 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 385 GLN
C 190 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.219414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.147527 restraints weight = 6362.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.154968 restraints weight = 3179.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.159672 restraints weight = 2134.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.064   6450  Z= 0.339
  Angle     :  0.736   7.066   8682  Z= 0.392
  Chirality :  0.050   0.284    964
  Planarity :  0.006   0.058   1122
  Dihedral  :  6.752  56.171    852
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 22.28 %
    Favored  : 73.12 %
  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: -1.85 (0.28), residues: 776
  helix:  0.53 (0.42), residues: 138
  sheet: -0.89 (0.44), residues: 140
  loop : -1.96 (0.25), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP b 340 
 HIS   0.007   0.002   HIS B 322 
 PHE   0.019   0.002   PHE b 327 
 TYR   0.014   0.002   TYR C  37 
 ARG   0.006   0.001   ARG b 352 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04003 (  187)
  hydrogen bonds       : angle       5.31541 (  519)
  covalent geometry    : bond        0.00768 ( 6450)
  covalent geometry    : angle       0.73622 ( 8682)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 243
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 GLU cc_start: 0.7367 (tt0) cc_final: 0.6798 (tt0)
REVERT: A  283 GLN cc_start: 0.7599 (tm-30) cc_final: 0.6538 (tm-30)
REVERT: B  374 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6539 (mtm110)
REVERT: a  225 LYS cc_start: 0.8942 (tttt) cc_final: 0.8389 (mmtp)
REVERT: a  241 GLU cc_start: 0.8575 (mp0) cc_final: 0.8300 (mp0)
REVERT: a  250 GLU cc_start: 0.7998 (pm20) cc_final: 0.7525 (pm20)
REVERT: a  251 GLN cc_start: 0.7936 (mt0) cc_final: 0.7638 (mp10)
REVERT: a  283 GLN cc_start: 0.7460 (tm-30) cc_final: 0.6766 (tm-30)
REVERT: a  296 LYS cc_start: 0.8454 (tppt) cc_final: 0.7671 (mttt)
REVERT: b  322 HIS cc_start: 0.7558 (OUTLIER) cc_final: 0.7264 (m-70)
REVERT: b  374 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.6484 (mtm110)
REVERT: C   34 GLU cc_start: 0.7076 (mp0) cc_final: 0.6817 (mp0)
REVERT: C   50 ASN cc_start: 0.7192 (m110) cc_final: 0.6890 (m110)
REVERT: C  164 GLU cc_start: 0.5516 (tp30) cc_final: 0.5231 (tp30)
REVERT: c   34 GLU cc_start: 0.7034 (mp0) cc_final: 0.6784 (mp0)
REVERT: c   50 ASN cc_start: 0.5981 (m110) cc_final: 0.5640 (m110)
  outliers start: 33
  outliers final: 25
  residues processed: 257
  average time/residue: 0.1995
  time to fit residues: 65.3117
Evaluate side-chains
  257 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 229
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  374 ARG
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain a residue  212 THR
Chi-restraints excluded: chain a residue  249 SER
Chi-restraints excluded: chain b residue  322 HIS
Chi-restraints excluded: chain b residue  334 THR
Chi-restraints excluded: chain b residue  348 VAL
Chi-restraints excluded: chain b residue  374 ARG
Chi-restraints excluded: chain b residue  383 ARG
Chi-restraints excluded: chain b residue  388 THR
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain C residue   46 SER
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue  108 SER
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue   49 ARG
Chi-restraints excluded: chain c residue   82 ILE
Chi-restraints excluded: chain c residue  108 SER
Chi-restraints excluded: chain c residue  142 VAL
Chi-restraints excluded: chain c residue  160 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 63 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0570
   chunk 39 optimal weight:    0.6980
   chunk 50 optimal weight:    0.3980
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.225638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.154074 restraints weight = 6321.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.162541 restraints weight = 2886.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.167859 restraints weight = 1847.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6855
moved from start:          0.2904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6450  Z= 0.127
  Angle     :  0.633   7.874   8682  Z= 0.323
  Chirality :  0.046   0.258    964
  Planarity :  0.004   0.056   1122
  Dihedral  :  6.324  58.855    852
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 24.65 %
    Favored  : 71.59 %
  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: -1.63 (0.28), residues: 776
  helix:  0.63 (0.43), residues: 138
  sheet: -0.91 (0.44), residues: 140
  loop : -1.72 (0.25), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP b 340 
 HIS   0.003   0.001   HIS A 248 
 PHE   0.014   0.001   PHE b 327 
 TYR   0.014   0.001   TYR C  37 
 ARG   0.003   0.000   ARG a 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03372 (  187)
  hydrogen bonds       : angle       4.89804 (  519)
  covalent geometry    : bond        0.00287 ( 6450)
  covalent geometry    : angle       0.63320 ( 8682)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 224
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 GLN cc_start: 0.7414 (tm-30) cc_final: 0.6360 (tm-30)
REVERT: B  370 PHE cc_start: 0.7857 (m-10) cc_final: 0.7633 (m-10)
REVERT: a  225 LYS cc_start: 0.8923 (tttt) cc_final: 0.8330 (mttm)
REVERT: a  241 GLU cc_start: 0.8518 (mp0) cc_final: 0.8234 (mp0)
REVERT: a  283 GLN cc_start: 0.7338 (tm-30) cc_final: 0.6459 (tm-30)
REVERT: a  296 LYS cc_start: 0.8456 (tppt) cc_final: 0.7669 (mttt)
REVERT: b  370 PHE cc_start: 0.7897 (m-10) cc_final: 0.7640 (m-10)
REVERT: C   34 GLU cc_start: 0.6944 (mp0) cc_final: 0.5905 (mp0)
REVERT: C   50 ASN cc_start: 0.7057 (m110) cc_final: 0.6742 (m110)
REVERT: c   34 GLU cc_start: 0.6932 (mp0) cc_final: 0.6499 (mp0)
REVERT: c  164 GLU cc_start: 0.5353 (tp30) cc_final: 0.4986 (tp30)
  outliers start: 27
  outliers final: 22
  residues processed: 238
  average time/residue: 0.1982
  time to fit residues: 60.0036
Evaluate side-chains
  238 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 216
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain a residue  171 GLU
Chi-restraints excluded: chain a residue  249 SER
Chi-restraints excluded: chain b residue  322 HIS
Chi-restraints excluded: chain b residue  334 THR
Chi-restraints excluded: chain b residue  388 THR
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain b residue  393 THR
Chi-restraints excluded: chain C residue   46 SER
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue   49 ARG
Chi-restraints excluded: chain c residue  142 VAL
Chi-restraints excluded: chain c residue  160 PHE
Chi-restraints excluded: chain c residue  161 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 65 optimal weight:    0.3980
   chunk 2 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 45 optimal weight:   10.0000
   chunk 62 optimal weight:    5.9990
   chunk 66 optimal weight:    4.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.219090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.143159 restraints weight = 6116.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.151369 restraints weight = 2934.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.156636 restraints weight = 1930.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6855
moved from start:          0.3298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6450  Z= 0.191
  Angle     :  0.668   8.531   8682  Z= 0.342
  Chirality :  0.047   0.255    964
  Planarity :  0.005   0.056   1122
  Dihedral  :  6.181  59.514    848
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 24.65 %
    Favored  : 69.78 %
  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: -1.76 (0.28), residues: 776
  helix:  0.58 (0.42), residues: 138
  sheet: -1.15 (0.43), residues: 140
  loop : -1.78 (0.25), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP b 340 
 HIS   0.004   0.001   HIS B 322 
 PHE   0.018   0.001   PHE b 327 
 TYR   0.016   0.002   TYR C 156 
 ARG   0.003   0.000   ARG b 352 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03265 (  187)
  hydrogen bonds       : angle       4.82974 (  519)
  covalent geometry    : bond        0.00438 ( 6450)
  covalent geometry    : angle       0.66771 ( 8682)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 224
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 GLU cc_start: 0.7242 (tt0) cc_final: 0.6535 (tt0)
REVERT: A  283 GLN cc_start: 0.7416 (tm-30) cc_final: 0.6338 (tm-30)
REVERT: B  370 PHE cc_start: 0.8023 (m-10) cc_final: 0.7688 (m-10)
REVERT: a  225 LYS cc_start: 0.8989 (tttt) cc_final: 0.8258 (mmtp)
REVERT: a  241 GLU cc_start: 0.8537 (mp0) cc_final: 0.8200 (mp0)
REVERT: a  283 GLN cc_start: 0.7266 (tm-30) cc_final: 0.6460 (tm-30)
REVERT: a  296 LYS cc_start: 0.8442 (tppt) cc_final: 0.7651 (mttt)
REVERT: b  370 PHE cc_start: 0.7985 (m-10) cc_final: 0.7609 (m-10)
REVERT: C   34 GLU cc_start: 0.6934 (mp0) cc_final: 0.5737 (mp0)
REVERT: C   50 ASN cc_start: 0.6840 (m110) cc_final: 0.6532 (m110)
REVERT: c  164 GLU cc_start: 0.5368 (tp30) cc_final: 0.4981 (tp30)
  outliers start: 40
  outliers final: 31
  residues processed: 249
  average time/residue: 0.1935
  time to fit residues: 62.8017
Evaluate side-chains
  254 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 223
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  388 THR
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain a residue  171 GLU
Chi-restraints excluded: chain a residue  205 ASN
Chi-restraints excluded: chain a residue  249 SER
Chi-restraints excluded: chain b residue  322 HIS
Chi-restraints excluded: chain b residue  323 ILE
Chi-restraints excluded: chain b residue  334 THR
Chi-restraints excluded: chain b residue  348 VAL
Chi-restraints excluded: chain b residue  366 VAL
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain b residue  393 THR
Chi-restraints excluded: chain C residue   46 SER
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue  108 SER
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue   49 ARG
Chi-restraints excluded: chain c residue  108 SER
Chi-restraints excluded: chain c residue  142 VAL
Chi-restraints excluded: chain c residue  160 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 54 optimal weight:    8.9990
   chunk 58 optimal weight:    5.9990
   chunk 44 optimal weight:   10.0000
   chunk 13 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 52 optimal weight:    9.9990
   chunk 23 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.223097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.148469 restraints weight = 5995.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.157215 restraints weight = 2775.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.162967 restraints weight = 1769.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6771
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6450  Z= 0.133
  Angle     :  0.651   9.577   8682  Z= 0.327
  Chirality :  0.046   0.246    964
  Planarity :  0.004   0.056   1122
  Dihedral  :  6.051  59.574    848
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 25.49 %
    Favored  : 69.64 %
  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: -1.57 (0.28), residues: 776
  helix:  0.64 (0.42), residues: 138
  sheet: -1.12 (0.45), residues: 136
  loop : -1.57 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP b 340 
 HIS   0.004   0.001   HIS A 248 
 PHE   0.014   0.001   PHE b 327 
 TYR   0.016   0.002   TYR C 156 
 ARG   0.004   0.000   ARG C 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03037 (  187)
  hydrogen bonds       : angle       4.67662 (  519)
  covalent geometry    : bond        0.00306 ( 6450)
  covalent geometry    : angle       0.65121 ( 8682)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 225
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 GLU cc_start: 0.8042 (tt0) cc_final: 0.7596 (mp0)
REVERT: A  283 GLN cc_start: 0.7367 (tm-30) cc_final: 0.6322 (tm-30)
REVERT: B  370 PHE cc_start: 0.7931 (m-10) cc_final: 0.7628 (m-10)
REVERT: a  225 LYS cc_start: 0.8958 (tttt) cc_final: 0.8305 (mttm)
REVERT: a  241 GLU cc_start: 0.8539 (mp0) cc_final: 0.8218 (mp0)
REVERT: a  283 GLN cc_start: 0.7320 (tm-30) cc_final: 0.6163 (tm-30)
REVERT: a  296 LYS cc_start: 0.8430 (tppt) cc_final: 0.7664 (mttm)
REVERT: b  370 PHE cc_start: 0.7871 (m-10) cc_final: 0.7557 (m-10)
REVERT: C   34 GLU cc_start: 0.6996 (mp0) cc_final: 0.5834 (mp0)
REVERT: C   50 ASN cc_start: 0.6787 (m110) cc_final: 0.6476 (m110)
REVERT: C  140 ARG cc_start: 0.7757 (mpt-90) cc_final: 0.7484 (mpt90)
REVERT: c  122 MET cc_start: 0.5801 (ptt) cc_final: 0.5301 (ppp)
  outliers start: 35
  outliers final: 29
  residues processed: 245
  average time/residue: 0.2368
  time to fit residues: 75.2336
Evaluate side-chains
  249 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 220
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  388 THR
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain a residue  156 MET
Chi-restraints excluded: chain a residue  171 GLU
Chi-restraints excluded: chain a residue  249 SER
Chi-restraints excluded: chain a residue  276 LYS
Chi-restraints excluded: chain b residue  322 HIS
Chi-restraints excluded: chain b residue  323 ILE
Chi-restraints excluded: chain b residue  334 THR
Chi-restraints excluded: chain b residue  348 VAL
Chi-restraints excluded: chain b residue  366 VAL
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain b residue  393 THR
Chi-restraints excluded: chain C residue   46 SER
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue  108 SER
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue   49 ARG
Chi-restraints excluded: chain c residue  160 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0980
   chunk 22 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.223401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.150753 restraints weight = 5920.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.159431 restraints weight = 2719.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.165142 restraints weight = 1727.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6780
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6450  Z= 0.133
  Angle     :  0.674  10.344   8682  Z= 0.334
  Chirality :  0.046   0.238    964
  Planarity :  0.004   0.058   1122
  Dihedral  :  5.974  58.670    848
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 25.63 %
    Favored  : 69.36 %
  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: -1.62 (0.28), residues: 776
  helix:  0.68 (0.42), residues: 138
  sheet: -1.19 (0.44), residues: 140
  loop : -1.63 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP b 340 
 HIS   0.006   0.001   HIS A 237 
 PHE   0.015   0.001   PHE b 327 
 TYR   0.015   0.001   TYR C 156 
 ARG   0.003   0.000   ARG a 240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02942 (  187)
  hydrogen bonds       : angle       4.60474 (  519)
  covalent geometry    : bond        0.00308 ( 6450)
  covalent geometry    : angle       0.67378 ( 8682)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 222
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 GLN cc_start: 0.7398 (tm-30) cc_final: 0.6373 (tm-30)
REVERT: B  370 PHE cc_start: 0.7913 (m-10) cc_final: 0.7631 (m-10)
REVERT: a  225 LYS cc_start: 0.8966 (tttt) cc_final: 0.8340 (mttm)
REVERT: a  241 GLU cc_start: 0.8573 (mp0) cc_final: 0.8220 (mp0)
REVERT: a  283 GLN cc_start: 0.7318 (tm-30) cc_final: 0.6189 (tm-30)
REVERT: a  296 LYS cc_start: 0.8392 (tppt) cc_final: 0.7604 (mttm)
REVERT: b  370 PHE cc_start: 0.7865 (m-10) cc_final: 0.7566 (m-10)
REVERT: C   34 GLU cc_start: 0.7103 (mp0) cc_final: 0.6574 (mp0)
REVERT: C   50 ASN cc_start: 0.6717 (m110) cc_final: 0.6412 (m110)
REVERT: C  140 ARG cc_start: 0.8073 (mpt-90) cc_final: 0.7793 (mmt180)
REVERT: c   34 GLU cc_start: 0.6992 (mp0) cc_final: 0.6486 (mp0)
REVERT: c  122 MET cc_start: 0.5894 (ptt) cc_final: 0.5338 (ppp)
REVERT: c  176 LYS cc_start: 0.7983 (mmtt) cc_final: 0.6950 (mtmt)
  outliers start: 36
  outliers final: 32
  residues processed: 238
  average time/residue: 0.1979
  time to fit residues: 60.5159
Evaluate side-chains
  253 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 221
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain a residue  156 MET
Chi-restraints excluded: chain a residue  171 GLU
Chi-restraints excluded: chain a residue  249 SER
Chi-restraints excluded: chain a residue  272 SER
Chi-restraints excluded: chain a residue  276 LYS
Chi-restraints excluded: chain b residue  322 HIS
Chi-restraints excluded: chain b residue  323 ILE
Chi-restraints excluded: chain b residue  334 THR
Chi-restraints excluded: chain b residue  348 VAL
Chi-restraints excluded: chain b residue  366 VAL
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain b residue  393 THR
Chi-restraints excluded: chain C residue   46 SER
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue  108 SER
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue   49 ARG
Chi-restraints excluded: chain c residue   84 ILE
Chi-restraints excluded: chain c residue  108 SER
Chi-restraints excluded: chain c residue  142 VAL
Chi-restraints excluded: chain c residue  160 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 1 optimal weight:    0.8980
   chunk 64 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0070
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.9402

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.223822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.146314 restraints weight = 6017.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.155239 restraints weight = 2786.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.161067 restraints weight = 1792.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6795
moved from start:          0.3762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6450  Z= 0.144
  Angle     :  0.661   9.253   8682  Z= 0.329
  Chirality :  0.046   0.230    964
  Planarity :  0.005   0.058   1122
  Dihedral  :  5.963  57.700    848
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 26.32 %
    Favored  : 69.08 %
  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: -1.63 (0.28), residues: 776
  helix:  0.75 (0.42), residues: 138
  sheet: -1.34 (0.44), residues: 140
  loop : -1.61 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP b 340 
 HIS   0.003   0.001   HIS A 237 
 PHE   0.017   0.001   PHE b 327 
 TYR   0.010   0.001   TYR a 198 
 ARG   0.004   0.000   ARG a 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02908 (  187)
  hydrogen bonds       : angle       4.53596 (  519)
  covalent geometry    : bond        0.00333 ( 6450)
  covalent geometry    : angle       0.66067 ( 8682)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 217
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 GLN cc_start: 0.7386 (tm-30) cc_final: 0.6360 (tm-30)
REVERT: B  370 PHE cc_start: 0.7931 (m-10) cc_final: 0.7624 (m-10)
REVERT: a  225 LYS cc_start: 0.8987 (tttt) cc_final: 0.8287 (mmtp)
REVERT: a  241 GLU cc_start: 0.8560 (mp0) cc_final: 0.8213 (mp0)
REVERT: a  283 GLN cc_start: 0.7228 (tm-30) cc_final: 0.6108 (tm-30)
REVERT: a  296 LYS cc_start: 0.8351 (tppt) cc_final: 0.7554 (mttm)
REVERT: b  370 PHE cc_start: 0.7910 (m-10) cc_final: 0.7563 (m-10)
REVERT: C   34 GLU cc_start: 0.7129 (mp0) cc_final: 0.6568 (mp0)
REVERT: C   50 ASN cc_start: 0.6869 (m110) cc_final: 0.6562 (m110)
REVERT: C  157 GLU cc_start: 0.7334 (pp20) cc_final: 0.6785 (pt0)
REVERT: c   34 GLU cc_start: 0.7041 (mp0) cc_final: 0.6462 (mp0)
REVERT: c  122 MET cc_start: 0.5972 (ptt) cc_final: 0.5317 (ppp)
REVERT: c  140 ARG cc_start: 0.8210 (mpt90) cc_final: 0.7881 (mmt180)
REVERT: c  176 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7580 (mtmt)
  outliers start: 33
  outliers final: 31
  residues processed: 235
  average time/residue: 0.2022
  time to fit residues: 60.9815
Evaluate side-chains
  247 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 216
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain a residue  156 MET
Chi-restraints excluded: chain a residue  171 GLU
Chi-restraints excluded: chain a residue  276 LYS
Chi-restraints excluded: chain b residue  322 HIS
Chi-restraints excluded: chain b residue  323 ILE
Chi-restraints excluded: chain b residue  334 THR
Chi-restraints excluded: chain b residue  348 VAL
Chi-restraints excluded: chain b residue  366 VAL
Chi-restraints excluded: chain b residue  369 ILE
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain b residue  393 THR
Chi-restraints excluded: chain C residue   46 SER
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue  108 SER
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue   49 ARG
Chi-restraints excluded: chain c residue   84 ILE
Chi-restraints excluded: chain c residue  108 SER
Chi-restraints excluded: chain c residue  121 GLU
Chi-restraints excluded: chain c residue  142 VAL
Chi-restraints excluded: chain c residue  160 PHE
Chi-restraints excluded: chain c residue  165 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 52 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 63 optimal weight:    0.0000
   chunk 74 optimal weight:    8.9990
   chunk 75 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.225324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.149068 restraints weight = 6051.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.158132 restraints weight = 2751.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.164143 restraints weight = 1748.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6754
moved from start:          0.3883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6450  Z= 0.133
  Angle     :  0.682   9.251   8682  Z= 0.337
  Chirality :  0.046   0.223    964
  Planarity :  0.004   0.058   1122
  Dihedral  :  5.928  56.847    848
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 28.13 %
    Favored  : 67.97 %
  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: -1.56 (0.29), residues: 776
  helix:  0.81 (0.42), residues: 138
  sheet: -1.42 (0.43), residues: 140
  loop : -1.52 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP b 340 
 HIS   0.003   0.001   HIS A 237 
 PHE   0.015   0.001   PHE b 327 
 TYR   0.013   0.001   TYR C 156 
 ARG   0.004   0.000   ARG a 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02904 (  187)
  hydrogen bonds       : angle       4.58577 (  519)
  covalent geometry    : bond        0.00309 ( 6450)
  covalent geometry    : angle       0.68236 ( 8682)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 220
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 ASP cc_start: 0.8340 (t0) cc_final: 0.8135 (t0)
REVERT: A  283 GLN cc_start: 0.7403 (tm-30) cc_final: 0.6349 (tm-30)
REVERT: B  370 PHE cc_start: 0.7934 (m-10) cc_final: 0.7646 (m-10)
REVERT: a  225 LYS cc_start: 0.8986 (tttt) cc_final: 0.8264 (mmtp)
REVERT: a  241 GLU cc_start: 0.8589 (mp0) cc_final: 0.8231 (mp0)
REVERT: a  283 GLN cc_start: 0.7298 (tm-30) cc_final: 0.6152 (tm-30)
REVERT: a  296 LYS cc_start: 0.8349 (tppt) cc_final: 0.7572 (mttm)
REVERT: b  370 PHE cc_start: 0.7912 (m-10) cc_final: 0.7580 (m-10)
REVERT: C   34 GLU cc_start: 0.7123 (mp0) cc_final: 0.6545 (mp0)
REVERT: C   50 ASN cc_start: 0.6825 (m110) cc_final: 0.6513 (m110)
REVERT: C  157 GLU cc_start: 0.7447 (pp20) cc_final: 0.7028 (pt0)
REVERT: c   34 GLU cc_start: 0.7066 (mp0) cc_final: 0.6162 (mp0)
REVERT: c  122 MET cc_start: 0.5952 (ptt) cc_final: 0.5329 (ppp)
REVERT: c  176 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7533 (mtmt)
  outliers start: 28
  outliers final: 27
  residues processed: 235
  average time/residue: 0.2051
  time to fit residues: 62.0817
Evaluate side-chains
  246 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 219
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain a residue  156 MET
Chi-restraints excluded: chain a residue  171 GLU
Chi-restraints excluded: chain a residue  276 LYS
Chi-restraints excluded: chain b residue  322 HIS
Chi-restraints excluded: chain b residue  323 ILE
Chi-restraints excluded: chain b residue  334 THR
Chi-restraints excluded: chain b residue  348 VAL
Chi-restraints excluded: chain b residue  366 VAL
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain b residue  393 THR
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue  108 SER
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain c residue   49 ARG
Chi-restraints excluded: chain c residue  108 SER
Chi-restraints excluded: chain c residue  121 GLU
Chi-restraints excluded: chain c residue  142 VAL
Chi-restraints excluded: chain c residue  160 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 74 optimal weight:    9.9990
   chunk 20 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0070
   chunk 35 optimal weight:    2.9990
   chunk 72 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    1.6004

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.220875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.143408 restraints weight = 6036.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.151874 restraints weight = 2862.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.157371 restraints weight = 1862.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6847
moved from start:          0.4041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6450  Z= 0.205
  Angle     :  0.724   9.370   8682  Z= 0.361
  Chirality :  0.048   0.217    964
  Planarity :  0.005   0.059   1122
  Dihedral  :  6.148  58.479    848
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 27.99 %
    Favored  : 67.69 %
  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: -1.66 (0.29), residues: 776
  helix:  0.77 (0.42), residues: 138
  sheet: -1.54 (0.43), residues: 140
  loop : -1.58 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP b 340 
 HIS   0.004   0.001   HIS B 322 
 PHE   0.019   0.002   PHE b 327 
 TYR   0.013   0.002   TYR C 156 
 ARG   0.003   0.000   ARG a 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02988 (  187)
  hydrogen bonds       : angle       4.63748 (  519)
  covalent geometry    : bond        0.00476 ( 6450)
  covalent geometry    : angle       0.72426 ( 8682)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 227
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 GLN cc_start: 0.7418 (tm-30) cc_final: 0.6373 (tm-30)
REVERT: B  370 PHE cc_start: 0.8065 (m-10) cc_final: 0.7662 (m-10)
REVERT: a  225 LYS cc_start: 0.8977 (tttt) cc_final: 0.8249 (mmtp)
REVERT: a  241 GLU cc_start: 0.8593 (mp0) cc_final: 0.8250 (mp0)
REVERT: a  283 GLN cc_start: 0.7315 (tm-30) cc_final: 0.6227 (tm-30)
REVERT: a  296 LYS cc_start: 0.8305 (tppt) cc_final: 0.7550 (mttm)
REVERT: b  370 PHE cc_start: 0.7951 (m-10) cc_final: 0.7592 (m-10)
REVERT: C   34 GLU cc_start: 0.7178 (mp0) cc_final: 0.6585 (mp0)
REVERT: C   50 ASN cc_start: 0.6743 (m110) cc_final: 0.6412 (m110)
REVERT: C  157 GLU cc_start: 0.7543 (pp20) cc_final: 0.6933 (pt0)
REVERT: c   34 GLU cc_start: 0.7133 (mp0) cc_final: 0.6213 (mp0)
REVERT: c  122 MET cc_start: 0.5939 (ptt) cc_final: 0.5294 (ppp)
REVERT: c  140 ARG cc_start: 0.8136 (mpt90) cc_final: 0.7758 (mmt180)
REVERT: c  174 LEU cc_start: 0.9083 (tt) cc_final: 0.8596 (tp)
REVERT: c  176 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7574 (mtmt)
  outliers start: 31
  outliers final: 28
  residues processed: 244
  average time/residue: 0.2100
  time to fit residues: 65.9338
Evaluate side-chains
  250 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 222
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  383 ARG
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain a residue  156 MET
Chi-restraints excluded: chain a residue  171 GLU
Chi-restraints excluded: chain a residue  276 LYS
Chi-restraints excluded: chain b residue  322 HIS
Chi-restraints excluded: chain b residue  323 ILE
Chi-restraints excluded: chain b residue  334 THR
Chi-restraints excluded: chain b residue  348 VAL
Chi-restraints excluded: chain b residue  366 VAL
Chi-restraints excluded: chain b residue  388 THR
Chi-restraints excluded: chain b residue  389 THR
Chi-restraints excluded: chain b residue  393 THR
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain c residue   46 SER
Chi-restraints excluded: chain c residue   84 ILE
Chi-restraints excluded: chain c residue  108 SER
Chi-restraints excluded: chain c residue  121 GLU
Chi-restraints excluded: chain c residue  142 VAL
Chi-restraints excluded: chain c residue  160 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 65 optimal weight:    0.2980
   chunk 47 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 69 optimal weight:    7.9990
   chunk 17 optimal weight:    0.0040
   chunk 4 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 10 optimal weight:    0.3980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.4192

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 145 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.226285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.152960 restraints weight = 6097.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.162218 restraints weight = 2726.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.168426 restraints weight = 1697.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6783
moved from start:          0.4146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6450  Z= 0.125
  Angle     :  0.731   9.651   8682  Z= 0.360
  Chirality :  0.046   0.199    964
  Planarity :  0.005   0.065   1122
  Dihedral  :  5.275  57.909    844
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 29.25 %
    Favored  : 66.85 %
  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: -1.44 (0.29), residues: 776
  helix:  0.76 (0.42), residues: 138
  sheet: -1.41 (0.46), residues: 136
  loop : -1.37 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP b 340 
 HIS   0.004   0.001   HIS A 237 
 PHE   0.011   0.001   PHE C  83 
 TYR   0.012   0.001   TYR C 156 
 ARG   0.007   0.001   ARG c  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02983 (  187)
  hydrogen bonds       : angle       4.69138 (  519)
  covalent geometry    : bond        0.00287 ( 6450)
  covalent geometry    : angle       0.73088 ( 8682)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3117.54 seconds
wall clock time: 55 minutes 5.82 seconds (3305.82 seconds total)