Starting phenix.real_space_refine
on Wed Feb  4 04:54:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9q2r_72173/02_2026/9q2r_72173.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9q2r_72173/02_2026/9q2r_72173.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9q2r_72173/02_2026/9q2r_72173.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9q2r_72173/02_2026/9q2r_72173.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9q2r_72173/02_2026/9q2r_72173.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9q2r_72173/02_2026/9q2r_72173.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      36      5.16       5
     C    5738      2.51       5
     N    1404      2.21       5
     O    1562      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8744
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 2030
          Classifications: {'peptide': 251}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 243}
    Chain: "B"
      Number of atoms: 2030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 2030
          Classifications: {'peptide': 251}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 243}
    Chain: "C"
      Number of atoms: 2315
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2315
          Classifications: {'peptide': 290}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 283}
    Chain: "D"
      Number of atoms: 2315
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2315
          Classifications: {'peptide': 290}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 283}
    Chain: "C"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.16, per 1000 atoms: 0.25
  Number of scatterers: 8744
  At special positions: 0
  Unit cell: (75.6, 87.75, 141.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     P       4     15.00
     O    1562      8.00
     N    1404      7.00
     C    5738      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: 0.69
  Conformation dependent library (CDL) restraints added in 350.2 milliseconds
  

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2044

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 9 sheets defined
      63.5% alpha, 9.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid -4 through 17
    Processing helix  chain 'A' and resid 17 through 40
      removed outlier: 4.378A  pdb=" N   TYR A  21 " --> pdb=" O   SER A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 81
      removed outlier: 4.871A  pdb=" N   ASP A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 87
      removed outlier: 3.803A  pdb=" N   TYR A  86 " --> pdb=" O   THR A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 126
    Processing helix  chain 'A' and resid 132 through 162
    Processing helix  chain 'A' and resid 164 through 186
      removed outlier: 4.585A  pdb=" N   VAL A 178 " --> pdb=" O   LEU A 174 " (cutoff:3.500A)
      Proline residue:  A 179  - end of helix
      Proline residue:  A 183  - end of helix
    Processing helix  chain 'A' and resid 191 through 199
    Processing helix  chain 'A' and resid 202 through 210
    Processing helix  chain 'A' and resid 219 through 242
    Processing helix  chain 'B' and resid -3 through 16
    Processing helix  chain 'B' and resid 17 through 40
      removed outlier: 4.074A  pdb=" N   TYR B  21 " --> pdb=" O   SER B  17 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ASN B  40 " --> pdb=" O   ILE B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 81
      removed outlier: 4.641A  pdb=" N   VAL B  54 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   ASP B  77 " --> pdb=" O   THR B  73 " (cutoff:3.500A)
      removed outlier: 5.086A  pdb=" N   PHE B  78 " --> pdb=" O   ILE B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 86
    Processing helix  chain 'B' and resid 89 through 126
    Processing helix  chain 'B' and resid 132 through 162
    Processing helix  chain 'B' and resid 164 through 186
      removed outlier: 4.803A  pdb=" N   VAL B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
      Proline residue:  B 179  - end of helix
      Proline residue:  B 183  - end of helix
    Processing helix  chain 'B' and resid 191 through 199
    Processing helix  chain 'B' and resid 202 through 210
    Processing helix  chain 'B' and resid 219 through 242
    Processing helix  chain 'C' and resid 38 through 48
    Processing helix  chain 'C' and resid 79 through 91
    Processing helix  chain 'C' and resid 96 through 108
    Processing helix  chain 'C' and resid 109 through 113
    Processing helix  chain 'C' and resid 116 through 120
    Processing helix  chain 'C' and resid 121 through 135
    Processing helix  chain 'C' and resid 151 through 169
    Processing helix  chain 'C' and resid 179 through 184
    Processing helix  chain 'C' and resid 218 through 233
      removed outlier: 3.576A  pdb=" N   ASP C 223 " --> pdb=" O   HIS C 219 " (cutoff:3.500A)
      removed outlier: 5.243A  pdb=" N   ARG C 224 " --> pdb=" O   LYS C 220 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 253 through 263
    Processing helix  chain 'C' and resid 276 through 290
      removed outlier: 5.416A  pdb=" N   ARG C 287 " --> pdb=" O   ASN C 283 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   GLY C 288 " --> pdb=" O   ILE C 284 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 38 through 48
    Processing helix  chain 'D' and resid 79 through 91
    Processing helix  chain 'D' and resid 96 through 108
    Processing helix  chain 'D' and resid 109 through 113
    Processing helix  chain 'D' and resid 116 through 120
    Processing helix  chain 'D' and resid 121 through 135
    Processing helix  chain 'D' and resid 151 through 169
    Processing helix  chain 'D' and resid 179 through 184
    Processing helix  chain 'D' and resid 221 through 233
    Processing helix  chain 'D' and resid 253 through 263
    Processing helix  chain 'D' and resid 276 through 290
      removed outlier: 4.571A  pdb=" N   ARG D 287 " --> pdb=" O   ASN D 283 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   GLY D 288 " --> pdb=" O   ILE D 284 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 19 through 22
      removed outlier: 5.335A  pdb=" N   ILE C  19 " --> pdb=" O   HIS C   5 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU C   3 " --> pdb=" O   PHE C  21 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LYS C  56 " --> pdb=" O   GLU C   4 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 9 through 10
    Processing sheet with id=AA3, first strand: chain 'C' and resid 65 through 68
      removed outlier: 4.015A  pdb=" N   GLY C  66 " --> pdb=" O   PHE C 140 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ILE C 142 " --> pdb=" O   GLY C  66 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   VAL C  29 " --> pdb=" O   ILE C 175 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ARG C 189 " --> pdb=" O   ILE C  28 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE C  32 " --> pdb=" O   VAL C 191 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU C 193 " --> pdb=" O   ILE C  32 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   GLN C 200 " --> pdb=" O   PHE C 192 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   ARG C 194 " --> pdb=" O   PHE C 198 " (cutoff:3.500A)
      removed outlier: 5.320A  pdb=" N   PHE C 198 " --> pdb=" O   ARG C 194 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 235 through 239
      removed outlier: 8.326A  pdb=" N   LEU C 235 " --> pdb=" O   ASN C 248 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   ASN C 248 " --> pdb=" O   LEU C 235 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   TYR C 269 " --> pdb=" O   THR C 216 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 21 through 22
    Processing sheet with id=AA6, first strand: chain 'D' and resid 7 through 10
      removed outlier: 6.252A  pdb=" N   LYS D   8 " --> pdb=" O   VAL D  15 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 65 through 68
      removed outlier: 6.001A  pdb=" N   LEU D 141 " --> pdb=" O   LEU D 174 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   SER D 176 " --> pdb=" O   LEU D 141 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LEU D 143 " --> pdb=" O   SER D 176 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   VAL D  29 " --> pdb=" O   ILE D 175 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   ILE D  28 " --> pdb=" O   ARG D 189 " (cutoff:3.500A)
      removed outlier: 8.155A  pdb=" N   VAL D 191 " --> pdb=" O   ILE D  28 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   GLY D  30 " --> pdb=" O   VAL D 191 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   LEU D 193 " --> pdb=" O   GLY D  30 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   ILE D  32 " --> pdb=" O   LEU D 193 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLN D 200 " --> pdb=" O   PHE D 192 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ARG D 194 " --> pdb=" O   PHE D 198 " (cutoff:3.500A)
      removed outlier: 5.226A  pdb=" N   PHE D 198 " --> pdb=" O   ARG D 194 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 212 through 216
      removed outlier: 3.670A  pdb=" N   TYR D 269 " --> pdb=" O   THR D 216 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 235 through 239

    551 hydrogen bonds defined for protein.
    1593 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: 1.20

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1377
        1.31 -     1.44: 2351
        1.44 -     1.57: 5117
        1.57 -     1.69: 11
        1.69 -     1.82: 70
  Bond restraints: 8926
  Sorted by residual:
  bond pdb=" CA  ASP D 239 "
       pdb=" CB  ASP D 239 "
    ideal  model  delta    sigma   weight residual
    1.529  1.694 -0.165 1.54e-02 4.22e+03 1.14e+02
  bond pdb=" CA  VAL C 217 "
       pdb=" CB  VAL C 217 "
    ideal  model  delta    sigma   weight residual
    1.551  1.605 -0.054 1.08e-02 8.57e+03 2.53e+01
  bond pdb=" CG1 ILE C 173 "
       pdb=" CD1 ILE C 173 "
    ideal  model  delta    sigma   weight residual
    1.513  1.387  0.126 3.90e-02 6.57e+02 1.04e+01
  bond pdb=" CA  VAL D 217 "
       pdb=" CB  VAL D 217 "
    ideal  model  delta    sigma   weight residual
    1.544  1.592 -0.047 1.49e-02 4.50e+03 1.01e+01
  bond pdb=" C   ILE B 181 "
       pdb=" N   LYS B 182 "
    ideal  model  delta    sigma   weight residual
    1.332  1.377 -0.044 1.50e-02 4.44e+03 8.72e+00
  ... (remaining 8921 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.93: 11495
        3.93 -     7.86: 473
        7.86 -    11.79: 81
       11.79 -    15.72: 15
       15.72 -    19.65: 2
  Bond angle restraints: 12066
  Sorted by residual:
  angle pdb=" CA  LYS A 135 "
        pdb=" CB  LYS A 135 "
        pdb=" CG  LYS A 135 "
      ideal   model   delta    sigma   weight residual
     114.10  128.22  -14.12 2.00e+00 2.50e-01 4.99e+01
  angle pdb=" N   GLU C 262 "
        pdb=" CA  GLU C 262 "
        pdb=" CB  GLU C 262 "
      ideal   model   delta    sigma   weight residual
     110.39  121.04  -10.65 1.66e+00 3.63e-01 4.11e+01
  angle pdb=" C   ASN C 285 "
        pdb=" N   GLN C 286 "
        pdb=" CA  GLN C 286 "
      ideal   model   delta    sigma   weight residual
     122.06  110.93   11.13 1.86e+00 2.89e-01 3.58e+01
  angle pdb=" CA  TYR B   9 "
        pdb=" CB  TYR B   9 "
        pdb=" CG  TYR B   9 "
      ideal   model   delta    sigma   weight residual
     113.90  103.24   10.66 1.80e+00 3.09e-01 3.51e+01
  angle pdb=" C   ARG D 224 "
        pdb=" CA  ARG D 224 "
        pdb=" CB  ARG D 224 "
      ideal   model   delta    sigma   weight residual
     110.85  120.91  -10.06 1.70e+00 3.46e-01 3.50e+01
  ... (remaining 12061 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.17: 5138
       29.17 -    58.33: 173
       58.33 -    87.50: 9
       87.50 -   116.66: 2
      116.66 -   145.83: 2
  Dihedral angle restraints: 5324
    sinusoidal: 2156
      harmonic: 3168
  Sorted by residual:
  dihedral pdb=" C2' ADP C 301 "
           pdb=" C1' ADP C 301 "
           pdb=" N9  ADP C 301 "
           pdb=" C4  ADP C 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
      91.55  -54.28  145.83     1      2.00e+01 2.50e-03 4.39e+01
  dihedral pdb=" O1B ADP C 301 "
           pdb=" O3A ADP C 301 "
           pdb=" PB  ADP C 301 "
           pdb=" PA  ADP C 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   79.81 -139.81     1      2.00e+01 2.50e-03 4.23e+01
  dihedral pdb=" C   LYS A 135 "
           pdb=" N   LYS A 135 "
           pdb=" CA  LYS A 135 "
           pdb=" CB  LYS A 135 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.34   13.74     0      2.50e+00 1.60e-01 3.02e+01
  ... (remaining 5321 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.177: 1307
       0.177 -    0.354: 87
       0.354 -    0.531: 9
       0.531 -    0.708: 2
       0.708 -    0.885: 1
  Chirality restraints: 1406
  Sorted by residual:
  chirality pdb=" CB  THR C 212 "
            pdb=" CA  THR C 212 "
            pdb=" OG1 THR C 212 "
            pdb=" CG2 THR C 212 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    1.67    0.88 2.00e-01 2.50e+01 1.96e+01
  chirality pdb=" CB  ILE C 186 "
            pdb=" CA  ILE C 186 "
            pdb=" CG1 ILE C 186 "
            pdb=" CG2 ILE C 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.01    0.64 2.00e-01 2.50e+01 1.02e+01
  chirality pdb=" CB  ILE A  74 "
            pdb=" CA  ILE A  74 "
            pdb=" CG1 ILE A  74 "
            pdb=" CG2 ILE A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.04    0.60 2.00e-01 2.50e+01 9.05e+00
  ... (remaining 1403 not shown)

  Planarity restraints: 1472
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B   9 "   -0.041 2.00e-02 2.50e+03   3.48e-02 2.43e+01
        pdb=" CG  TYR B   9 "    0.083 2.00e-02 2.50e+03
        pdb=" CD1 TYR B   9 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR B   9 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR B   9 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B   9 "   -0.028 2.00e-02 2.50e+03
        pdb=" CZ  TYR B   9 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR B   9 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 217 "   -0.023 2.00e-02 2.50e+03   4.77e-02 2.27e+01
        pdb=" C   ASP B 217 "    0.082 2.00e-02 2.50e+03
        pdb=" O   ASP B 217 "   -0.032 2.00e-02 2.50e+03
        pdb=" N   PHE B 218 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  64 "   -0.024 2.00e-02 2.50e+03   4.69e-02 2.20e+01
        pdb=" C   ILE B  64 "    0.081 2.00e-02 2.50e+03
        pdb=" O   ILE B  64 "   -0.030 2.00e-02 2.50e+03
        pdb=" N   ILE B  65 "   -0.027 2.00e-02 2.50e+03
  ... (remaining 1469 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1397
        2.77 -     3.30: 8479
        3.30 -     3.84: 14074
        3.84 -     4.37: 15078
        4.37 -     4.90: 27017
  Nonbonded interactions: 66045
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D 253 "
            pdb=" OG1 THR D 272 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OG  SER B 213 "
            pdb=" O   ASN B 215 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" O   PRO D 152 "
            pdb=" OG  SER D 155 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OG1 THR C  40 "
            pdb=" O2A ADP C 301 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   LYS C  34 "
            pdb=" NZ  LYS C  39 "
     model   vdw
     2.331 3.120
  ... (remaining 66040 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 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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:             0.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.390
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
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      :  0.009   0.165   8926  Z= 0.438
  Angle     :  1.810  19.654  12066  Z= 0.980
  Chirality :  0.101   0.885   1406
  Planarity :  0.009   0.068   1472
  Dihedral  : 14.594 145.826   3280
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  3.26 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.12 %
    Favored  : 95.77 %
  Cbeta Deviations :  1.57 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.25), residues: 1074
  helix:  1.62 (0.20), residues: 604
  sheet:  2.09 (0.60), residues: 82
  loop : -1.80 (0.28), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 224 
 TYR   0.083   0.005   TYR B   9 
 PHE   0.053   0.004   PHE C 282 
 TRP   0.026   0.002   TRP A  60 
 HIS   0.021   0.003   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00883 ( 8926)
  covalent geometry    : angle       1.80984 (12066)
  hydrogen bonds       : bond        0.11263 (  551)
  hydrogen bonds       : angle       5.80325 ( 1593)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 273
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ASN cc_start: 0.7612 (m110) cc_final: 0.7270 (m110)
REVERT: A   42 MET cc_start: 0.3623 (mtt) cc_final: 0.3398 (mtt)
REVERT: B   84 GLN cc_start: 0.7276 (mt0) cc_final: 0.6709 (mt0)
REVERT: C   43 MET cc_start: 0.7366 (mpp) cc_final: 0.7061 (mtm)
REVERT: C  274 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7569 (tppt)
REVERT: D   70 GLU cc_start: 0.8333 (pm20) cc_final: 0.7530 (tp30)
REVERT: D  122 MET cc_start: 0.7478 (tpt) cc_final: 0.6675 (tpp)
REVERT: D  278 ARG cc_start: 0.8973 (ttt90) cc_final: 0.8227 (mtm110)
  outliers start: 1
  outliers final: 1
  residues processed: 274
  average time/residue: 0.0877
  time to fit residues: 34.1952
Evaluate side-chains
  210 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 209
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.0270
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
C 197 HIS
C 200 GLN
D   5 HIS
** D  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 203 ASN
D 234 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.152291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.129563 restraints weight = 18335.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.130246 restraints weight = 12958.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.131097 restraints weight = 10670.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.131968 restraints weight = 8787.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.132098 restraints weight = 8126.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8926  Z= 0.149
  Angle     :  0.759   8.798  12066  Z= 0.394
  Chirality :  0.047   0.211   1406
  Planarity :  0.004   0.051   1472
  Dihedral  :  9.010 149.184   1178
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  3.30 %
    Favored  : 95.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.25), residues: 1074
  helix:  1.57 (0.20), residues: 619
  sheet:  1.24 (0.58), residues: 82
  loop : -2.03 (0.27), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 194 
 TYR   0.024   0.002   TYR B 206 
 PHE   0.020   0.001   PHE C 282 
 TRP   0.012   0.001   TRP B  60 
 HIS   0.011   0.001   HIS A   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8926)
  covalent geometry    : angle       0.75945 (12066)
  hydrogen bonds       : bond        0.05187 (  551)
  hydrogen bonds       : angle       4.96998 ( 1593)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 249
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ASN cc_start: 0.7685 (m110) cc_final: 0.7396 (m110)
REVERT: A   96 TYR cc_start: 0.8620 (t80) cc_final: 0.8167 (t80)
REVERT: C  124 MET cc_start: 0.7674 (mtt) cc_final: 0.7435 (mtp)
REVERT: C  278 ARG cc_start: 0.8250 (ttm-80) cc_final: 0.7836 (ttm-80)
  outliers start: 9
  outliers final: 2
  residues processed: 252
  average time/residue: 0.0786
  time to fit residues: 28.9920
Evaluate side-chains
  208 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 206
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   chunk 104 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 72 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 84 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
B  84 GLN
C 136 ASN
C 200 GLN
C 232 HIS
** D  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 126 GLN
** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.144652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.119757 restraints weight = 17674.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.121994 restraints weight = 11140.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.123520 restraints weight = 8045.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.124545 restraints weight = 6376.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.124986 restraints weight = 5457.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8926  Z= 0.179
  Angle     :  0.745   7.164  12066  Z= 0.384
  Chirality :  0.047   0.234   1406
  Planarity :  0.004   0.065   1472
  Dihedral  :  8.913 161.025   1178
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  6.08 %
    Favored  : 93.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.25), residues: 1074
  helix:  1.55 (0.20), residues: 623
  sheet:  0.88 (0.57), residues: 82
  loop : -2.03 (0.28), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 194 
 TYR   0.023   0.002   TYR B 206 
 PHE   0.026   0.002   PHE B 143 
 TRP   0.013   0.002   TRP B  60 
 HIS   0.012   0.002   HIS C 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 8926)
  covalent geometry    : angle       0.74462 (12066)
  hydrogen bonds       : bond        0.05033 (  551)
  hydrogen bonds       : angle       4.80578 ( 1593)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 243
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ASN cc_start: 0.7840 (m110) cc_final: 0.7482 (m110)
REVERT: A  211 MET cc_start: 0.6253 (ttp) cc_final: 0.6050 (ttp)
REVERT: C   43 MET cc_start: 0.8481 (mmm) cc_final: 0.8101 (mmm)
REVERT: D   68 LEU cc_start: 0.8656 (tp) cc_final: 0.8455 (tp)
REVERT: D  224 ARG cc_start: 0.6535 (mtm110) cc_final: 0.6177 (mmp-170)
REVERT: D  266 TYR cc_start: 0.6246 (m-10) cc_final: 0.5775 (m-80)
  outliers start: 4
  outliers final: 1
  residues processed: 246
  average time/residue: 0.0767
  time to fit residues: 27.5126
Evaluate side-chains
  199 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 198
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0980
   chunk 11 optimal weight:    0.5980
   chunk 23 optimal weight:    4.9990
   chunk 77 optimal weight:    0.3980
   chunk 3 optimal weight:    4.9990
   chunk 19 optimal weight:   10.0000
   chunk 39 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
B  84 GLN
C  49 ASN
C 136 ASN
C 200 GLN
C 232 HIS
D 126 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.147808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.122716 restraints weight = 17736.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.125121 restraints weight = 10965.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.126684 restraints weight = 7775.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.127758 restraints weight = 6136.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.128534 restraints weight = 5207.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.2596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8926  Z= 0.136
  Angle     :  0.704   7.018  12066  Z= 0.358
  Chirality :  0.046   0.237   1406
  Planarity :  0.004   0.061   1472
  Dihedral  :  8.817 162.459   1178
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  2.89 %
    Favored  : 96.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.25), residues: 1074
  helix:  1.62 (0.21), residues: 624
  sheet:  0.76 (0.57), residues: 82
  loop : -1.99 (0.29), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 278 
 TYR   0.037   0.002   TYR B   9 
 PHE   0.023   0.002   PHE A 199 
 TRP   0.013   0.001   TRP B  60 
 HIS   0.005   0.001   HIS A   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8926)
  covalent geometry    : angle       0.70438 (12066)
  hydrogen bonds       : bond        0.04568 (  551)
  hydrogen bonds       : angle       4.61934 ( 1593)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 250
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ASN cc_start: 0.7856 (m110) cc_final: 0.7565 (m110)
REVERT: A   38 MET cc_start: 0.4904 (tpt) cc_final: 0.4702 (tpt)
REVERT: A  173 PHE cc_start: 0.8506 (t80) cc_final: 0.8266 (t80)
REVERT: B  217 ASP cc_start: 0.6345 (t0) cc_final: 0.6121 (t0)
REVERT: C  110 ARG cc_start: 0.8128 (mmt90) cc_final: 0.7879 (mmt180)
REVERT: C  112 TYR cc_start: 0.6879 (p90) cc_final: 0.6181 (p90)
REVERT: C  124 MET cc_start: 0.8399 (mtm) cc_final: 0.7473 (mtt)
REVERT: C  200 GLN cc_start: 0.8218 (mt0) cc_final: 0.7931 (mt0)
REVERT: C  278 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7992 (ttm-80)
REVERT: D   86 LEU cc_start: 0.9059 (pp) cc_final: 0.8733 (pp)
REVERT: D  124 MET cc_start: 0.8178 (mtp) cc_final: 0.7875 (mtp)
REVERT: D  141 LEU cc_start: 0.8266 (mm) cc_final: 0.8049 (mm)
  outliers start: 4
  outliers final: 1
  residues processed: 253
  average time/residue: 0.0808
  time to fit residues: 29.5210
Evaluate side-chains
  202 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 201
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 81 optimal weight:    0.9990
   chunk 88 optimal weight:    6.9990
   chunk 14 optimal weight:    0.7980
   chunk 104 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 67 optimal weight:    5.9990
   chunk 100 optimal weight:   10.0000
   chunk 47 optimal weight:    0.2980
   overall best weight:    0.8186

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
A 139 ASN
C 136 ASN
D 126 GLN
D 244 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.147209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.122272 restraints weight = 18143.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.124601 restraints weight = 11439.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.126220 restraints weight = 8197.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.127204 restraints weight = 6478.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.128002 restraints weight = 5556.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8926  Z= 0.141
  Angle     :  0.715   7.754  12066  Z= 0.361
  Chirality :  0.046   0.257   1406
  Planarity :  0.004   0.065   1472
  Dihedral  :  8.746 163.940   1178
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.51 %
    Favored  : 96.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.25), residues: 1074
  helix:  1.63 (0.21), residues: 623
  sheet:  1.33 (0.58), residues: 72
  loop : -1.99 (0.29), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 278 
 TYR   0.034   0.001   TYR B   9 
 PHE   0.031   0.001   PHE B 143 
 TRP   0.016   0.001   TRP B  60 
 HIS   0.004   0.001   HIS C 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8926)
  covalent geometry    : angle       0.71495 (12066)
  hydrogen bonds       : bond        0.04444 (  551)
  hydrogen bonds       : angle       4.57759 ( 1593)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 245
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ASN cc_start: 0.7902 (m110) cc_final: 0.7559 (m110)
REVERT: A   42 MET cc_start: 0.3658 (mtt) cc_final: 0.3458 (mtt)
REVERT: A  173 PHE cc_start: 0.8531 (t80) cc_final: 0.8261 (t80)
REVERT: B   38 MET cc_start: 0.6159 (mmm) cc_final: 0.5271 (mmm)
REVERT: B  229 SER cc_start: 0.8513 (p) cc_final: 0.8311 (p)
REVERT: C  112 TYR cc_start: 0.6824 (p90) cc_final: 0.6164 (p90)
REVERT: C  124 MET cc_start: 0.8375 (mtm) cc_final: 0.7518 (mtt)
REVERT: D  124 MET cc_start: 0.8194 (mtp) cc_final: 0.7916 (mtp)
REVERT: D  266 TYR cc_start: 0.5140 (m-10) cc_final: 0.4804 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 247
  average time/residue: 0.0792
  time to fit residues: 28.3889
Evaluate side-chains
  197 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 89 optimal weight:    0.7980
   chunk 83 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 44 optimal weight:   10.0000
   chunk 49 optimal weight:    2.9990
   chunk 104 optimal weight:    9.9990
   chunk 50 optimal weight:    9.9990
   chunk 103 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0770
   chunk 63 optimal weight:    5.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 139 ASN
C  49 ASN
C 136 ASN
C 236 GLN
D 126 GLN
D 232 HIS
** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.148582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.125520 restraints weight = 17604.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.126024 restraints weight = 11632.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.126891 restraints weight = 9645.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.127313 restraints weight = 7999.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.127511 restraints weight = 7412.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8926  Z= 0.140
  Angle     :  0.712   7.433  12066  Z= 0.363
  Chirality :  0.046   0.271   1406
  Planarity :  0.004   0.060   1472
  Dihedral  :  8.743 167.459   1178
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.25), residues: 1074
  helix:  1.58 (0.20), residues: 623
  sheet:  1.22 (0.58), residues: 72
  loop : -1.97 (0.29), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 278 
 TYR   0.028   0.001   TYR B   9 
 PHE   0.037   0.002   PHE A 143 
 TRP   0.017   0.002   TRP B  60 
 HIS   0.005   0.001   HIS C 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8926)
  covalent geometry    : angle       0.71234 (12066)
  hydrogen bonds       : bond        0.04417 (  551)
  hydrogen bonds       : angle       4.59130 ( 1593)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ASN cc_start: 0.7934 (m110) cc_final: 0.7609 (m110)
REVERT: A  173 PHE cc_start: 0.8471 (t80) cc_final: 0.8237 (t80)
REVERT: B  157 ILE cc_start: 0.8527 (tp) cc_final: 0.8326 (tp)
REVERT: B  229 SER cc_start: 0.8548 (p) cc_final: 0.8312 (p)
REVERT: C   46 MET cc_start: 0.7239 (mtt) cc_final: 0.6627 (mtt)
REVERT: C  112 TYR cc_start: 0.6962 (p90) cc_final: 0.6265 (p90)
REVERT: C  124 MET cc_start: 0.8096 (mtm) cc_final: 0.7214 (mtt)
REVERT: C  278 ARG cc_start: 0.8056 (ttm-80) cc_final: 0.7637 (ttm-80)
REVERT: D  124 MET cc_start: 0.8163 (mtp) cc_final: 0.7961 (mtp)
REVERT: D  171 MET cc_start: 0.7201 (mmp) cc_final: 0.6941 (tpp)
REVERT: D  266 TYR cc_start: 0.5012 (m-10) cc_final: 0.4680 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 248
  average time/residue: 0.0807
  time to fit residues: 29.1053
Evaluate side-chains
  196 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 92 optimal weight:    0.0570
   chunk 44 optimal weight:    5.9990
   chunk 36 optimal weight:    0.5980
   chunk 106 optimal weight:    7.9990
   chunk 10 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
A 139 ASN
C  49 ASN
C 136 ASN
** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 126 GLN
** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 244 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.147693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.123016 restraints weight = 18042.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.125310 restraints weight = 11600.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.126855 restraints weight = 8435.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.127699 restraints weight = 6735.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.128551 restraints weight = 5844.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.3119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8926  Z= 0.137
  Angle     :  0.722   7.038  12066  Z= 0.363
  Chirality :  0.046   0.287   1406
  Planarity :  0.004   0.064   1472
  Dihedral  :  8.686 169.787   1178
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.25), residues: 1074
  helix:  1.60 (0.21), residues: 623
  sheet:  1.22 (0.58), residues: 72
  loop : -1.93 (0.29), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 278 
 TYR   0.032   0.001   TYR B   9 
 PHE   0.019   0.001   PHE B 143 
 TRP   0.023   0.002   TRP A  60 
 HIS   0.005   0.001   HIS C 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8926)
  covalent geometry    : angle       0.72178 (12066)
  hydrogen bonds       : bond        0.04273 (  551)
  hydrogen bonds       : angle       4.50664 ( 1593)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ASN cc_start: 0.7852 (m110) cc_final: 0.7528 (m110)
REVERT: A  155 PHE cc_start: 0.7407 (t80) cc_final: 0.6879 (t80)
REVERT: A  158 THR cc_start: 0.8167 (t) cc_final: 0.7902 (m)
REVERT: A  173 PHE cc_start: 0.8485 (t80) cc_final: 0.8272 (t80)
REVERT: B  229 SER cc_start: 0.8537 (p) cc_final: 0.8337 (p)
REVERT: C   43 MET cc_start: 0.8108 (mmm) cc_final: 0.7846 (mmm)
REVERT: C   46 MET cc_start: 0.7247 (mtt) cc_final: 0.6600 (mtt)
REVERT: C  112 TYR cc_start: 0.6741 (p90) cc_final: 0.6208 (p90)
REVERT: C  124 MET cc_start: 0.8120 (mtm) cc_final: 0.7101 (mtt)
REVERT: C  211 ASP cc_start: 0.6170 (m-30) cc_final: 0.5140 (t70)
REVERT: C  246 MET cc_start: 0.3641 (tmm) cc_final: 0.2920 (tpt)
REVERT: C  278 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7822 (ttm-80)
REVERT: D  171 MET cc_start: 0.7217 (mmp) cc_final: 0.6926 (tpp)
REVERT: D  266 TYR cc_start: 0.5195 (m-10) cc_final: 0.4772 (m-80)
REVERT: D  271 GLU cc_start: 0.7741 (pm20) cc_final: 0.7465 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 245
  average time/residue: 0.0826
  time to fit residues: 29.2098
Evaluate side-chains
  197 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 105 optimal weight:    8.9990
   chunk 70 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 87 optimal weight:    4.9990
   chunk 92 optimal weight:    0.0980
   chunk 46 optimal weight:    4.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
C  49 ASN
C 232 HIS
** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.147098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.122237 restraints weight = 18328.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.124231 restraints weight = 11907.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.125818 restraints weight = 8882.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.126702 restraints weight = 7130.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.127472 restraints weight = 6189.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.3285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8926  Z= 0.148
  Angle     :  0.731   7.499  12066  Z= 0.374
  Chirality :  0.046   0.299   1406
  Planarity :  0.004   0.063   1472
  Dihedral  :  8.664 171.795   1178
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.96 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.25), residues: 1074
  helix:  1.57 (0.21), residues: 622
  sheet:  1.15 (0.58), residues: 72
  loop : -1.92 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 278 
 TYR   0.024   0.001   TYR B   9 
 PHE   0.033   0.001   PHE B 143 
 TRP   0.017   0.002   TRP A 223 
 HIS   0.004   0.001   HIS C 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8926)
  covalent geometry    : angle       0.73145 (12066)
  hydrogen bonds       : bond        0.04371 (  551)
  hydrogen bonds       : angle       4.59288 ( 1593)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 244
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ASN cc_start: 0.7941 (m110) cc_final: 0.7631 (m110)
REVERT: A  155 PHE cc_start: 0.7446 (t80) cc_final: 0.6860 (t80)
REVERT: A  158 THR cc_start: 0.8140 (t) cc_final: 0.7879 (m)
REVERT: A  173 PHE cc_start: 0.8511 (t80) cc_final: 0.8310 (t80)
REVERT: B  229 SER cc_start: 0.8555 (p) cc_final: 0.8347 (p)
REVERT: C   43 MET cc_start: 0.8154 (mmm) cc_final: 0.7837 (mmm)
REVERT: C   46 MET cc_start: 0.7273 (mtt) cc_final: 0.6618 (mtt)
REVERT: C  112 TYR cc_start: 0.6755 (p90) cc_final: 0.6227 (p90)
REVERT: C  124 MET cc_start: 0.8435 (mtm) cc_final: 0.7488 (mtt)
REVERT: C  184 GLU cc_start: 0.8511 (pp20) cc_final: 0.8293 (pp20)
REVERT: C  226 GLU cc_start: 0.7383 (pm20) cc_final: 0.7120 (pm20)
REVERT: C  246 MET cc_start: 0.3682 (tmm) cc_final: 0.2813 (tpt)
REVERT: C  278 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7683 (ttm-80)
REVERT: D  266 TYR cc_start: 0.5287 (m-10) cc_final: 0.4796 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 244
  average time/residue: 0.0808
  time to fit residues: 28.6116
Evaluate side-chains
  189 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 74 optimal weight:    8.9990
   chunk 76 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0670
   chunk 1 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.8124

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

Flipped N/Q/H residues before XYZ refinement:
C  49 ASN
C 200 GLN
C 232 HIS
D 126 GLN
** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.146354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.121991 restraints weight = 18079.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.124245 restraints weight = 11483.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.125757 restraints weight = 8298.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.126750 restraints weight = 6623.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.127354 restraints weight = 5650.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8926  Z= 0.147
  Angle     :  0.736   9.379  12066  Z= 0.373
  Chirality :  0.046   0.302   1406
  Planarity :  0.004   0.066   1472
  Dihedral  :  8.642 173.980   1178
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.96 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.26), residues: 1074
  helix:  1.64 (0.21), residues: 622
  sheet:  1.09 (0.58), residues: 72
  loop : -1.86 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 278 
 TYR   0.023   0.002   TYR B   9 
 PHE   0.033   0.001   PHE A 143 
 TRP   0.022   0.002   TRP A  60 
 HIS   0.003   0.001   HIS A   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8926)
  covalent geometry    : angle       0.73553 (12066)
  hydrogen bonds       : bond        0.04311 (  551)
  hydrogen bonds       : angle       4.57485 ( 1593)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 238
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ASN cc_start: 0.7910 (m110) cc_final: 0.7607 (m110)
REVERT: A  155 PHE cc_start: 0.7383 (t80) cc_final: 0.6888 (t80)
REVERT: A  158 THR cc_start: 0.8181 (t) cc_final: 0.7870 (m)
REVERT: A  173 PHE cc_start: 0.8479 (t80) cc_final: 0.8279 (t80)
REVERT: B   12 TYR cc_start: 0.7651 (m-10) cc_final: 0.7444 (m-80)
REVERT: B   38 MET cc_start: 0.6691 (mmm) cc_final: 0.6076 (mmm)
REVERT: B  229 SER cc_start: 0.8516 (p) cc_final: 0.8266 (p)
REVERT: C   43 MET cc_start: 0.8152 (mmm) cc_final: 0.7807 (mmm)
REVERT: C   46 MET cc_start: 0.7561 (mtt) cc_final: 0.6936 (mtt)
REVERT: C  226 GLU cc_start: 0.7358 (pm20) cc_final: 0.6965 (pm20)
REVERT: C  239 ASP cc_start: 0.7698 (t70) cc_final: 0.7494 (t0)
REVERT: C  246 MET cc_start: 0.3624 (tmm) cc_final: 0.2717 (tpt)
REVERT: C  278 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7834 (ttm-80)
REVERT: D   70 GLU cc_start: 0.8625 (pm20) cc_final: 0.8222 (pm20)
REVERT: D   89 GLN cc_start: 0.7497 (pm20) cc_final: 0.6873 (pm20)
REVERT: D  171 MET cc_start: 0.7105 (mmp) cc_final: 0.6879 (tpp)
REVERT: D  266 TYR cc_start: 0.5113 (m-10) cc_final: 0.4591 (m-80)
REVERT: D  271 GLU cc_start: 0.7800 (pm20) cc_final: 0.7493 (pm20)
  outliers start: 1
  outliers final: 0
  residues processed: 239
  average time/residue: 0.0857
  time to fit residues: 29.3361
Evaluate side-chains
  185 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 96 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0040
   chunk 54 optimal weight:    0.2980
   chunk 52 optimal weight:    6.9990
   chunk 77 optimal weight:    7.9990
   chunk 36 optimal weight:    0.6980
   chunk 45 optimal weight:    0.3980
   chunk 58 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
A 139 ASN
C  49 ASN
** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.144670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.119022 restraints weight = 17079.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.121420 restraints weight = 10403.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.123058 restraints weight = 7270.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.124151 restraints weight = 5648.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.124767 restraints weight = 4749.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8926  Z= 0.143
  Angle     :  0.746   9.451  12066  Z= 0.380
  Chirality :  0.047   0.313   1406
  Planarity :  0.004   0.088   1472
  Dihedral  :  8.548 174.924   1178
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.26), residues: 1074
  helix:  1.56 (0.21), residues: 622
  sheet:  1.66 (0.62), residues: 60
  loop : -1.85 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 194 
 TYR   0.031   0.001   TYR B   9 
 PHE   0.024   0.001   PHE B 143 
 TRP   0.021   0.002   TRP A  60 
 HIS   0.003   0.001   HIS A   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8926)
  covalent geometry    : angle       0.74597 (12066)
  hydrogen bonds       : bond        0.04289 (  551)
  hydrogen bonds       : angle       4.67115 ( 1593)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ASN cc_start: 0.7847 (m110) cc_final: 0.7478 (m110)
REVERT: A  155 PHE cc_start: 0.7494 (t80) cc_final: 0.6815 (t80)
REVERT: A  158 THR cc_start: 0.8135 (t) cc_final: 0.7874 (m)
REVERT: B   12 TYR cc_start: 0.7690 (m-10) cc_final: 0.7458 (m-80)
REVERT: B  229 SER cc_start: 0.8538 (p) cc_final: 0.8321 (p)
REVERT: C   43 MET cc_start: 0.8171 (mmm) cc_final: 0.7814 (mmm)
REVERT: C   46 MET cc_start: 0.7495 (mtt) cc_final: 0.7053 (mtt)
REVERT: C  226 GLU cc_start: 0.7519 (pm20) cc_final: 0.7085 (pm20)
REVERT: C  239 ASP cc_start: 0.7674 (t70) cc_final: 0.7424 (t0)
REVERT: C  246 MET cc_start: 0.3613 (tmm) cc_final: 0.2717 (tpt)
REVERT: D   70 GLU cc_start: 0.8739 (pm20) cc_final: 0.8243 (pm20)
REVERT: D  126 GLN cc_start: 0.7904 (mt0) cc_final: 0.7644 (mt0)
REVERT: D  166 VAL cc_start: 0.8776 (t) cc_final: 0.8555 (p)
REVERT: D  171 MET cc_start: 0.7095 (mmp) cc_final: 0.6836 (tpp)
REVERT: D  266 TYR cc_start: 0.4851 (m-10) cc_final: 0.4288 (m-80)
REVERT: D  271 GLU cc_start: 0.7760 (pm20) cc_final: 0.7473 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 241
  average time/residue: 0.0825
  time to fit residues: 28.6204
Evaluate side-chains
  188 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 102 optimal weight:    7.9990
   chunk 36 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 28 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 99 optimal weight:    8.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
C  49 ASN
C 232 HIS
** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.138399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.112063 restraints weight = 17447.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.114287 restraints weight = 10851.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.115774 restraints weight = 7732.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.116653 restraints weight = 6153.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.117344 restraints weight = 5302.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.3850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   8926  Z= 0.198
  Angle     :  0.810   9.565  12066  Z= 0.417
  Chirality :  0.050   0.327   1406
  Planarity :  0.004   0.064   1472
  Dihedral  :  8.671 178.285   1178
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.25), residues: 1074
  helix:  1.31 (0.21), residues: 628
  sheet:  1.46 (0.63), residues: 60
  loop : -2.02 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 278 
 TYR   0.026   0.002   TYR B   9 
 PHE   0.032   0.002   PHE A 143 
 TRP   0.019   0.003   TRP A 223 
 HIS   0.007   0.001   HIS C  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 8926)
  covalent geometry    : angle       0.80972 (12066)
  hydrogen bonds       : bond        0.04905 (  551)
  hydrogen bonds       : angle       4.83916 ( 1593)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1430.58 seconds
wall clock time: 25 minutes 39.81 seconds (1539.81 seconds total)