Starting phenix.real_space_refine
on Wed Feb  4 04:15:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9q2n_72169/02_2026/9q2n_72169.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9q2n_72169/02_2026/9q2n_72169.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9q2n_72169/02_2026/9q2n_72169.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9q2n_72169/02_2026/9q2n_72169.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9q2n_72169/02_2026/9q2n_72169.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9q2n_72169/02_2026/9q2n_72169.cif"
  }
  resolution = 4.3
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    5698      2.51       5
     N    1390      2.21       5
     O    1538      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 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: 8662
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 2016
          Classifications: {'peptide': 249}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 242}
    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: "B"
      Number of atoms: 2016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 2016
          Classifications: {'peptide': 249}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 242}
    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}
  Time building chain proxies: 1.47, per 1000 atoms: 0.17
  Number of scatterers: 8662
  At special positions: 0
  Unit cell: (88.4, 80.6, 139.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1538      8.00
     N    1390      7.00
     C    5698      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: 0.62
  Conformation dependent library (CDL) restraints added in 298.9 milliseconds
  

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2036

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 7 sheets defined
      63.4% alpha, 9.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid -2 through 17
      removed outlier: 3.961A  pdb=" N   SER A  17 " --> pdb=" O   SER A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 17 through 40
      removed outlier: 4.430A  pdb=" N   TYR A  21 " --> pdb=" O   SER A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 81
      removed outlier: 4.874A  pdb=" N   ASP A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      removed outlier: 4.941A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 86
    Processing helix  chain 'A' and resid 89 through 126
    Processing helix  chain 'A' and resid 132 through 162
      removed outlier: 3.822A  pdb=" N   TYR A 136 " --> pdb=" O   ALA A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 186
      removed outlier: 4.718A  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 213
      removed outlier: 4.701A  pdb=" N   ILE A 212 " --> pdb=" O   THR A 208 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   SER A 213 " --> pdb=" O   ASP A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 242
    Processing helix  chain 'C' and resid 38 through 48
    Processing helix  chain 'C' and resid 79 through 92
    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 136
      removed outlier: 3.752A  pdb=" N   ASN C 136 " --> pdb=" O   VAL C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 151 through 169
    Processing helix  chain 'C' and resid 179 through 186
    Processing helix  chain 'C' and resid 218 through 233
      removed outlier: 4.935A  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 286
      removed outlier: 4.543A  pdb=" N   THR C 280 " --> pdb=" O   SER C 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid -1 through 16
    Processing helix  chain 'B' and resid 17 through 40
      removed outlier: 4.324A  pdb=" N   TYR B  21 " --> pdb=" O   SER B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 81
      removed outlier: 4.327A  pdb=" N   VAL B  54 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   ASP B  77 " --> pdb=" O   THR B  73 " (cutoff:3.500A)
      removed outlier: 5.066A  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
      removed outlier: 3.697A  pdb=" N   TYR B 136 " --> pdb=" O   ALA B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 186
      removed outlier: 4.596A  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 '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 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 218 through 233
      removed outlier: 4.604A  pdb=" N   ASP D 223 " --> pdb=" O   HIS D 219 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   ARG D 224 " --> pdb=" O   LYS D 220 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 253 through 263
    Processing helix  chain 'D' and resid 276 through 290
      removed outlier: 4.299A  pdb=" N   ARG D 287 " --> pdb=" O   ASN D 283 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   GLY D 288 " --> pdb=" O   ILE D 284 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ASP D 289 " --> pdb=" O   ASN D 285 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LYS D 290 " --> pdb=" O   GLN D 286 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 19 through 21
      removed outlier: 5.376A  pdb=" N   ILE C  19 " --> pdb=" O   HIS C   5 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   GLU C   4 " --> pdb=" O   LYS C  56 " (cutoff:3.500A)
      removed outlier: 4.607A  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 67
      removed outlier: 6.619A  pdb=" N   GLY C  66 " --> pdb=" O   ILE C 142 " (cutoff:3.500A)
      removed outlier: 8.436A  pdb=" N   ASP C 144 " --> pdb=" O   GLY C  66 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   LEU C 141 " --> pdb=" O   LEU C 174 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   SER C 176 " --> pdb=" O   LEU C 141 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   LEU C 143 " --> pdb=" O   SER C 176 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   VAL C  29 " --> pdb=" O   ILE C 175 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   ILE C  28 " --> pdb=" O   ARG C 189 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   VAL C 191 " --> pdb=" O   ILE C  28 " (cutoff:3.500A)
      removed outlier: 5.801A  pdb=" N   GLY C  30 " --> pdb=" O   VAL C 191 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   LEU C 193 " --> pdb=" O   GLY C  30 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ILE C  32 " --> pdb=" O   LEU C 193 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   ALA C 190 " --> pdb=" O   ASP C 201 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   ASP C 201 " --> pdb=" O   ALA C 190 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   PHE C 192 " --> pdb=" O   VAL C 199 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 238 through 239
      removed outlier: 4.209A  pdb=" N   LEU C 245 " --> pdb=" O   THR C 213 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   THR C 213 " --> pdb=" O   LEU C 245 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLU C 271 " --> pdb=" O   ILE C 214 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 13 through 21
      removed outlier: 6.815A  pdb=" N   VAL D  15 " --> pdb=" O   LYS D   9 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   LYS D   9 " --> pdb=" O   VAL D  15 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ASN D  17 " --> pdb=" O   THR D   7 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   THR D   7 " --> pdb=" O   ASN D  17 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   ILE D  19 " --> pdb=" O   HIS D   5 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   GLU D   4 " --> pdb=" O   LYS D  56 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   LYS D  56 " --> pdb=" O   GLU D   4 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 65 through 68
      removed outlier: 6.731A  pdb=" N   GLY D  66 " --> pdb=" O   ILE D 142 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   ASP D 144 " --> pdb=" O   GLY D  66 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   LEU D  68 " --> pdb=" O   ASP D 144 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   LEU D 141 " --> pdb=" O   LEU D 174 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   SER D 176 " --> pdb=" O   LEU D 141 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   LEU D 143 " --> pdb=" O   SER D 176 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ILE D  28 " --> pdb=" O   ARG D 189 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   VAL D 191 " --> pdb=" O   ILE D  28 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   GLY D  30 " --> pdb=" O   VAL D 191 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   LEU D 193 " --> pdb=" O   GLY D  30 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   ILE D  32 " --> pdb=" O   LEU D 193 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ALA D 190 " --> pdb=" O   ASP D 201 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   ASP D 201 " --> pdb=" O   ALA D 190 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   PHE D 192 " --> pdb=" O   VAL D 199 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 238 through 239
      removed outlier: 3.669A  pdb=" N   TYR D 269 " --> pdb=" O   THR D 216 " (cutoff:3.500A)

    526 hydrogen bonds defined for protein.
    1521 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: 0.77

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1400
        1.32 -     1.44: 2306
        1.44 -     1.57: 5059
        1.57 -     1.69: 3
        1.69 -     1.82: 70
  Bond restraints: 8838
  Sorted by residual:
  bond pdb=" CG1 ILE C 142 "
       pdb=" CD1 ILE C 142 "
    ideal  model  delta    sigma   weight residual
    1.513  1.348  0.165 3.90e-02 6.57e+02 1.79e+01
  bond pdb=" CG  PRO D 267 "
       pdb=" CD  PRO D 267 "
    ideal  model  delta    sigma   weight residual
    1.503  1.368  0.135 3.40e-02 8.65e+02 1.57e+01
  bond pdb=" CG1 ILE C 104 "
       pdb=" CD1 ILE C 104 "
    ideal  model  delta    sigma   weight residual
    1.513  1.384  0.129 3.90e-02 6.57e+02 1.09e+01
  bond pdb=" C   ILE A 181 "
       pdb=" N   LYS A 182 "
    ideal  model  delta    sigma   weight residual
    1.332  1.380 -0.047 1.50e-02 4.44e+03 9.93e+00
  bond pdb=" CB  PRO D 267 "
       pdb=" CG  PRO D 267 "
    ideal  model  delta    sigma   weight residual
    1.492  1.644 -0.152 5.00e-02 4.00e+02 9.23e+00
  ... (remaining 8833 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.37: 11498
        4.37 -     8.73: 374
        8.73 -    13.10: 51
       13.10 -    17.47: 5
       17.47 -    21.83: 4
  Bond angle restraints: 11932
  Sorted by residual:
  angle pdb=" CA  PRO D 267 "
        pdb=" N   PRO D 267 "
        pdb=" CD  PRO D 267 "
      ideal   model   delta    sigma   weight residual
     112.00   94.32   17.68 1.40e+00 5.10e-01 1.59e+02
  angle pdb=" CB  MET A 211 "
        pdb=" CG  MET A 211 "
        pdb=" SD  MET A 211 "
      ideal   model   delta    sigma   weight residual
     112.70  134.53  -21.83 3.00e+00 1.11e-01 5.30e+01
  angle pdb=" N   MET A 211 "
        pdb=" CA  MET A 211 "
        pdb=" CB  MET A 211 "
      ideal   model   delta    sigma   weight residual
     110.16  120.57  -10.41 1.48e+00 4.57e-01 4.94e+01
  angle pdb=" C   ILE C  50 "
        pdb=" N   ILE C  51 "
        pdb=" CA  ILE C  51 "
      ideal   model   delta    sigma   weight residual
     121.85  130.09   -8.24 1.19e+00 7.06e-01 4.79e+01
  angle pdb=" CA  LYS D 258 "
        pdb=" CB  LYS D 258 "
        pdb=" CG  LYS D 258 "
      ideal   model   delta    sigma   weight residual
     114.10  127.56  -13.46 2.00e+00 2.50e-01 4.53e+01
  ... (remaining 11927 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 4710
       17.81 -    35.62: 488
       35.62 -    53.43: 70
       53.43 -    71.24: 10
       71.24 -    89.04: 4
  Dihedral angle restraints: 5282
    sinusoidal: 2126
      harmonic: 3156
  Sorted by residual:
  dihedral pdb=" CA  ILE D  69 "
           pdb=" C   ILE D  69 "
           pdb=" N   GLU D  70 "
           pdb=" CA  GLU D  70 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -125.96  -54.04     0      5.00e+00 4.00e-02 1.17e+02
  dihedral pdb=" C   PHE D  53 "
           pdb=" N   PHE D  53 "
           pdb=" CA  PHE D  53 "
           pdb=" CB  PHE D  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.83   12.23     0      2.50e+00 1.60e-01 2.39e+01
  dihedral pdb=" C   PHE C  53 "
           pdb=" N   PHE C  53 "
           pdb=" CA  PHE C  53 "
           pdb=" CB  PHE C  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.85  -11.75     0      2.50e+00 1.60e-01 2.21e+01
  ... (remaining 5279 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.124: 1135
       0.124 -    0.248: 216
       0.248 -    0.372: 32
       0.372 -    0.496: 7
       0.496 -    0.620: 2
  Chirality restraints: 1392
  Sorted by residual:
  chirality pdb=" CB  ILE C 142 "
            pdb=" CA  ILE C 142 "
            pdb=" CG1 ILE C 142 "
            pdb=" CG2 ILE C 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.02    0.62 2.00e-01 2.50e+01 9.62e+00
  chirality pdb=" CG  LEU C 174 "
            pdb=" CB  LEU C 174 "
            pdb=" CD1 LEU C 174 "
            pdb=" CD2 LEU C 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.01   -0.58 2.00e-01 2.50e+01 8.32e+00
  chirality pdb=" CB  VAL C 166 "
            pdb=" CA  VAL C 166 "
            pdb=" CG1 VAL C 166 "
            pdb=" CG2 VAL C 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.17   -0.46 2.00e-01 2.50e+01 5.18e+00
  ... (remaining 1389 not shown)

  Planarity restraints: 1464
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR D 266 "    0.136 5.00e-02 4.00e+02   1.87e-01 5.61e+01
        pdb=" N   PRO D 267 "   -0.323 5.00e-02 4.00e+02
        pdb=" CA  PRO D 267 "    0.100 5.00e-02 4.00e+02
        pdb=" CD  PRO D 267 "    0.087 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D 290 "   -0.032 2.00e-02 2.50e+03   6.18e-02 3.82e+01
        pdb=" C   LYS D 290 "    0.107 2.00e-02 2.50e+03
        pdb=" O   LYS D 290 "   -0.038 2.00e-02 2.50e+03
        pdb=" OXT LYS D 290 "   -0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  81 "   -0.028 2.00e-02 2.50e+03   5.55e-02 3.08e+01
        pdb=" C   GLY A  81 "    0.096 2.00e-02 2.50e+03
        pdb=" O   GLY A  81 "   -0.035 2.00e-02 2.50e+03
        pdb=" N   THR A  82 "   -0.033 2.00e-02 2.50e+03
  ... (remaining 1461 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 352
        2.71 -     3.26: 8457
        3.26 -     3.80: 13646
        3.80 -     4.35: 16597
        4.35 -     4.90: 27777
  Nonbonded interactions: 66829
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 219 "
            pdb=" OE1 GLN A 222 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" OG  SER B 219 "
            pdb=" OE1 GLN B 222 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OG1 THR D 212 "
            pdb=" O   ARG D 273 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   THR D 212 "
            pdb=" OG1 THR D 272 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OD1 ASP D 211 "
            pdb=" OG  SER D 275 "
     model   vdw
     2.278 3.040
  ... (remaining 66824 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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:             0.270
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.390
  Find NCS groups from input model:        0.080
  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:0.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5803
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   8838  Z= 0.426
  Angle     :  1.776  21.833  11932  Z= 0.995
  Chirality :  0.104   0.620   1392
  Planarity :  0.010   0.187   1464
  Dihedral  : 13.943  89.045   3246
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.46 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Cbeta Deviations :  0.79 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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:  0.75 (0.25), residues: 1070
  helix:  1.56 (0.21), residues: 603
  sheet:  2.29 (0.56), residues: 85
  loop : -1.76 (0.28), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A   2 
 TYR   0.082   0.005   TYR D  82 
 PHE   0.077   0.006   PHE A 199 
 TRP   0.031   0.002   TRP A 141 
 HIS   0.022   0.003   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00890 ( 8838)
  covalent geometry    : angle       1.77598 (11932)
  hydrogen bonds       : bond        0.10340 (  526)
  hydrogen bonds       : angle       5.97729 ( 1521)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.0858 (tmm) cc_final: 0.0375 (tmm)
REVERT: A  156 LEU cc_start: 0.7754 (tp) cc_final: 0.7550 (tt)
REVERT: A  237 ASN cc_start: 0.6885 (m-40) cc_final: 0.5994 (m110)
REVERT: C   93 LYS cc_start: 0.6636 (mptt) cc_final: 0.6322 (tptp)
REVERT: C  242 ASP cc_start: 0.4458 (t0) cc_final: 0.3820 (m-30)
REVERT: C  258 LYS cc_start: 0.6092 (ttmm) cc_final: 0.5755 (ptpp)
REVERT: C  267 PRO cc_start: 0.6696 (Cg_endo) cc_final: 0.6046 (Cg_exo)
REVERT: B   15 PHE cc_start: 0.5483 (m-10) cc_final: 0.5179 (m-10)
REVERT: B   83 ILE cc_start: 0.8668 (tp) cc_final: 0.8200 (tp)
REVERT: B  166 MET cc_start: 0.7940 (tpp) cc_final: 0.7677 (tpp)
REVERT: B  223 TRP cc_start: 0.5218 (t60) cc_final: 0.4907 (t60)
REVERT: D   89 GLN cc_start: 0.7746 (mm110) cc_final: 0.7520 (mt0)
REVERT: D  171 MET cc_start: 0.6541 (ppp) cc_final: 0.4660 (mtt)
REVERT: D  246 MET cc_start: 0.2578 (ttt) cc_final: 0.2190 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.0656
  time to fit residues: 20.7527
Evaluate side-chains
  166 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0170
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
A   5 ASN
C 136 ASN
C 200 GLN
** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 200 GLN
D 250 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.178882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.161807 restraints weight = 18860.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.162419 restraints weight = 14422.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.164044 restraints weight = 12161.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.164448 restraints weight = 9376.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.164758 restraints weight = 8526.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.4206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5870
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8838  Z= 0.149
  Angle     :  0.684   8.540  11932  Z= 0.370
  Chirality :  0.046   0.176   1392
  Planarity :  0.005   0.088   1464
  Dihedral  :  5.040  37.010   1152
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  6.63 %
    Favored  : 92.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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:  0.21 (0.24), residues: 1070
  helix:  1.10 (0.19), residues: 612
  sheet:  1.71 (0.54), residues: 87
  loop : -1.93 (0.28), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 224 
 TYR   0.024   0.002   TYR A 206 
 PHE   0.025   0.002   PHE B 146 
 TRP   0.009   0.001   TRP A 141 
 HIS   0.003   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 8838)
  covalent geometry    : angle       0.68381 (11932)
  hydrogen bonds       : bond        0.04725 (  526)
  hydrogen bonds       : angle       5.05370 ( 1521)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 205
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6659 (t) cc_final: 0.6400 (t)
REVERT: A   42 MET cc_start: 0.1778 (pmm) cc_final: 0.1196 (pmm)
REVERT: A  104 ILE cc_start: 0.7719 (mm) cc_final: 0.7427 (mm)
REVERT: A  156 LEU cc_start: 0.7711 (tp) cc_final: 0.7424 (tt)
REVERT: A  237 ASN cc_start: 0.6959 (m-40) cc_final: 0.6658 (m110)
REVERT: C  204 MET cc_start: 0.5733 (ppp) cc_final: 0.5208 (mmp)
REVERT: C  258 LYS cc_start: 0.6208 (ttmm) cc_final: 0.5939 (ptpp)
REVERT: C  267 PRO cc_start: 0.6548 (Cg_endo) cc_final: 0.5833 (Cg_exo)
REVERT: B   68 MET cc_start: 0.6738 (ttt) cc_final: 0.6090 (tmt)
REVERT: B   83 ILE cc_start: 0.8712 (tp) cc_final: 0.8371 (tp)
REVERT: B  166 MET cc_start: 0.7845 (tpp) cc_final: 0.7564 (tpp)
REVERT: D   53 PHE cc_start: 0.3727 (p90) cc_final: 0.3328 (p90)
REVERT: D  171 MET cc_start: 0.6563 (ppp) cc_final: 0.4757 (mtp)
REVERT: D  173 ILE cc_start: 0.7661 (mt) cc_final: 0.7455 (mm)
  outliers start: 4
  outliers final: 1
  residues processed: 208
  average time/residue: 0.0565
  time to fit residues: 17.3580
Evaluate side-chains
  153 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 69 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 37 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0970
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A   5 ASN
** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  89 GLN
D 200 GLN
D 250 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.176199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.157770 restraints weight = 18970.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.158593 restraints weight = 16758.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.159341 restraints weight = 12666.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.159661 restraints weight = 11789.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.159833 restraints weight = 10651.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.4142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5959
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8838  Z= 0.143
  Angle     :  0.647   8.000  11932  Z= 0.351
  Chirality :  0.045   0.225   1392
  Planarity :  0.004   0.058   1464
  Dihedral  :  4.923  37.707   1152
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.97 %
    Favored  : 94.93 %
  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:  0.03 (0.24), residues: 1070
  helix:  0.98 (0.19), residues: 611
  sheet:  1.28 (0.53), residues: 87
  loop : -1.96 (0.28), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 273 
 TYR   0.026   0.002   TYR A 206 
 PHE   0.030   0.002   PHE B 143 
 TRP   0.009   0.001   TRP B 223 
 HIS   0.009   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8838)
  covalent geometry    : angle       0.64667 (11932)
  hydrogen bonds       : bond        0.04344 (  526)
  hydrogen bonds       : angle       4.82476 ( 1521)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 202
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 MET cc_start: 0.1082 (pmm) cc_final: 0.0810 (pmm)
REVERT: A   86 TYR cc_start: 0.7480 (m-80) cc_final: 0.7131 (m-10)
REVERT: A  104 ILE cc_start: 0.7798 (mm) cc_final: 0.7557 (mm)
REVERT: A  237 ASN cc_start: 0.7108 (m-40) cc_final: 0.6808 (m-40)
REVERT: C   27 ARG cc_start: 0.5548 (mmp80) cc_final: 0.4897 (mmm-85)
REVERT: C  145 GLU cc_start: 0.5686 (tp30) cc_final: 0.5109 (mm-30)
REVERT: C  204 MET cc_start: 0.6206 (ppp) cc_final: 0.5715 (mmp)
REVERT: C  267 PRO cc_start: 0.6797 (Cg_endo) cc_final: 0.6045 (Cg_exo)
REVERT: B   68 MET cc_start: 0.6685 (ttt) cc_final: 0.6115 (tmt)
REVERT: B   77 ASP cc_start: 0.7907 (m-30) cc_final: 0.7679 (m-30)
REVERT: B   83 ILE cc_start: 0.8910 (tp) cc_final: 0.8658 (tp)
REVERT: B  155 PHE cc_start: 0.6058 (t80) cc_final: 0.5808 (t80)
REVERT: B  166 MET cc_start: 0.7884 (tpp) cc_final: 0.7570 (tpp)
REVERT: D   53 PHE cc_start: 0.3984 (p90) cc_final: 0.3564 (p90)
REVERT: D   89 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7648 (mt0)
REVERT: D  128 LEU cc_start: 0.8254 (tp) cc_final: 0.8031 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 203
  average time/residue: 0.0572
  time to fit residues: 17.0412
Evaluate side-chains
  150 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 72 optimal weight:    0.3980
   chunk 69 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A   5 ASN
C 200 GLN
** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 250 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.175607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.157834 restraints weight = 19477.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.158487 restraints weight = 17146.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.159182 restraints weight = 14343.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.159713 restraints weight = 12017.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.159953 restraints weight = 10678.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5976
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8838  Z= 0.140
  Angle     :  0.629   7.794  11932  Z= 0.338
  Chirality :  0.045   0.175   1392
  Planarity :  0.004   0.063   1464
  Dihedral  :  4.900  35.273   1152
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.90 %
    Favored  : 97.00 %
  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: -0.02 (0.24), residues: 1070
  helix:  0.97 (0.19), residues: 613
  sheet:  0.98 (0.53), residues: 88
  loop : -1.99 (0.29), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 110 
 TYR   0.026   0.002   TYR A 206 
 PHE   0.038   0.002   PHE D 140 
 TRP   0.010   0.001   TRP B 223 
 HIS   0.004   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8838)
  covalent geometry    : angle       0.62921 (11932)
  hydrogen bonds       : bond        0.04086 (  526)
  hydrogen bonds       : angle       4.74774 ( 1521)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 198
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 ILE cc_start: 0.7858 (mm) cc_final: 0.7611 (mm)
REVERT: A  156 LEU cc_start: 0.7801 (tt) cc_final: 0.7189 (tp)
REVERT: C  145 GLU cc_start: 0.5626 (tp30) cc_final: 0.5121 (mm-30)
REVERT: C  204 MET cc_start: 0.6402 (ppp) cc_final: 0.6001 (mmp)
REVERT: C  267 PRO cc_start: 0.7090 (Cg_endo) cc_final: 0.6450 (Cg_exo)
REVERT: B   68 MET cc_start: 0.6601 (ttt) cc_final: 0.6290 (tmt)
REVERT: B   77 ASP cc_start: 0.7909 (m-30) cc_final: 0.7653 (m-30)
REVERT: B  166 MET cc_start: 0.7532 (tpp) cc_final: 0.7172 (tpp)
REVERT: D   53 PHE cc_start: 0.4165 (p90) cc_final: 0.3739 (p90)
REVERT: D   63 ASP cc_start: 0.8017 (m-30) cc_final: 0.7764 (m-30)
REVERT: D  109 MET cc_start: 0.6073 (mmt) cc_final: 0.5836 (mmt)
REVERT: D  165 LEU cc_start: 0.8143 (mt) cc_final: 0.7848 (mt)
REVERT: D  171 MET cc_start: 0.5879 (ppp) cc_final: 0.4071 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 198
  average time/residue: 0.0662
  time to fit residues: 18.7492
Evaluate side-chains
  146 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 80 optimal weight:    7.9990
   chunk 78 optimal weight:    7.9990
   chunk 35 optimal weight:    0.6980
   chunk 74 optimal weight:   10.0000
   chunk 36 optimal weight:    0.7980
   chunk 81 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A   5 ASN
C 126 GLN
C 200 GLN
** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 286 GLN
D 200 GLN
D 250 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.173467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.155835 restraints weight = 19379.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.155822 restraints weight = 17623.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.156720 restraints weight = 16138.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.156923 restraints weight = 12861.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.157329 restraints weight = 12442.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6049
moved from start:          0.2900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8838  Z= 0.144
  Angle     :  0.630   8.064  11932  Z= 0.338
  Chirality :  0.045   0.213   1392
  Planarity :  0.004   0.057   1464
  Dihedral  :  4.862  32.288   1152
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  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: -0.14 (0.24), residues: 1070
  helix:  0.86 (0.20), residues: 612
  sheet:  0.77 (0.54), residues: 87
  loop : -1.96 (0.29), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 224 
 TYR   0.025   0.002   TYR A 206 
 PHE   0.036   0.002   PHE D 140 
 TRP   0.012   0.001   TRP B 223 
 HIS   0.013   0.001   HIS D 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8838)
  covalent geometry    : angle       0.62993 (11932)
  hydrogen bonds       : bond        0.04061 (  526)
  hydrogen bonds       : angle       4.68739 ( 1521)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A  104 ILE cc_start: 0.7861 (mm) cc_final: 0.7639 (mm)
REVERT: A  156 LEU cc_start: 0.7724 (tt) cc_final: 0.7328 (tp)
REVERT: C   27 ARG cc_start: 0.6002 (mmp80) cc_final: 0.5169 (mmm-85)
REVERT: C  204 MET cc_start: 0.6424 (ppp) cc_final: 0.6005 (mmp)
REVERT: C  267 PRO cc_start: 0.7245 (Cg_endo) cc_final: 0.6629 (Cg_exo)
REVERT: B   68 MET cc_start: 0.6643 (ttt) cc_final: 0.6324 (tmt)
REVERT: B   77 ASP cc_start: 0.8065 (m-30) cc_final: 0.7796 (m-30)
REVERT: B  166 MET cc_start: 0.7563 (tpp) cc_final: 0.7174 (tpp)
REVERT: D   53 PHE cc_start: 0.4756 (p90) cc_final: 0.4365 (p90)
REVERT: D   63 ASP cc_start: 0.7970 (m-30) cc_final: 0.7746 (m-30)
REVERT: D  109 MET cc_start: 0.6093 (mmt) cc_final: 0.5821 (mmt)
REVERT: D  165 LEU cc_start: 0.8193 (mt) cc_final: 0.7850 (mt)
REVERT: D  171 MET cc_start: 0.5594 (ppp) cc_final: 0.5068 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.0552
  time to fit residues: 15.0813
Evaluate side-chains
  148 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 103 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 83 optimal weight:    7.9990
   chunk 92 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0370
   chunk 43 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.7062

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

Flipped N/Q/H residues before XYZ refinement:
A   5 ASN
C 178 HIS
C 200 GLN
** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 250 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.173362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.155345 restraints weight = 18767.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.155688 restraints weight = 16664.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.156456 restraints weight = 13628.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.157345 restraints weight = 11674.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.157426 restraints weight = 10752.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6048
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8838  Z= 0.137
  Angle     :  0.625   8.196  11932  Z= 0.335
  Chirality :  0.044   0.233   1392
  Planarity :  0.004   0.063   1464
  Dihedral  :  4.849  36.613   1152
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.08 (0.24), residues: 1070
  helix:  0.93 (0.20), residues: 610
  sheet:  0.77 (0.54), residues: 85
  loop : -1.93 (0.29), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 273 
 TYR   0.030   0.002   TYR D  99 
 PHE   0.033   0.002   PHE D 140 
 TRP   0.011   0.001   TRP B 223 
 HIS   0.004   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8838)
  covalent geometry    : angle       0.62492 (11932)
  hydrogen bonds       : bond        0.03907 (  526)
  hydrogen bonds       : angle       4.66471 ( 1521)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A   29 SER cc_start: 0.6782 (t) cc_final: 0.6581 (t)
REVERT: A  156 LEU cc_start: 0.7691 (tt) cc_final: 0.7257 (tp)
REVERT: C  204 MET cc_start: 0.6506 (ppp) cc_final: 0.6229 (mmp)
REVERT: C  267 PRO cc_start: 0.7231 (Cg_endo) cc_final: 0.6598 (Cg_exo)
REVERT: B   68 MET cc_start: 0.6618 (ttt) cc_final: 0.6200 (tmt)
REVERT: B   77 ASP cc_start: 0.8057 (m-30) cc_final: 0.7784 (m-30)
REVERT: B  139 ASN cc_start: 0.5442 (t0) cc_final: 0.4753 (t0)
REVERT: B  166 MET cc_start: 0.7632 (tpp) cc_final: 0.7199 (tpp)
REVERT: D   53 PHE cc_start: 0.4557 (p90) cc_final: 0.4209 (p90)
REVERT: D   63 ASP cc_start: 0.8034 (m-30) cc_final: 0.7748 (m-30)
REVERT: D  109 MET cc_start: 0.6021 (mmt) cc_final: 0.5762 (mmt)
REVERT: D  171 MET cc_start: 0.5497 (ppp) cc_final: 0.4763 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.0630
  time to fit residues: 17.1705
Evaluate side-chains
  146 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 33 optimal weight:    0.2980
   chunk 43 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0670
   chunk 91 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 80 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   chunk 16 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.5720

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

Flipped N/Q/H residues before XYZ refinement:
A   5 ASN
C 200 GLN
** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 200 GLN
** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 250 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.173961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.157786 restraints weight = 18999.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.157709 restraints weight = 17088.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.158850 restraints weight = 15234.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.159063 restraints weight = 12750.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.159174 restraints weight = 10890.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.4135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5985
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8838  Z= 0.127
  Angle     :  0.612   7.350  11932  Z= 0.328
  Chirality :  0.044   0.238   1392
  Planarity :  0.004   0.063   1464
  Dihedral  :  4.755  36.156   1152
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  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:  0.01 (0.24), residues: 1070
  helix:  1.03 (0.20), residues: 609
  sheet:  0.76 (0.55), residues: 85
  loop : -1.90 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 273 
 TYR   0.026   0.002   TYR D  99 
 PHE   0.034   0.002   PHE A 143 
 TRP   0.011   0.001   TRP B 223 
 HIS   0.003   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8838)
  covalent geometry    : angle       0.61180 (11932)
  hydrogen bonds       : bond        0.03818 (  526)
  hydrogen bonds       : angle       4.64614 ( 1521)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6879 (t) cc_final: 0.6649 (t)
REVERT: A   31 ILE cc_start: 0.8320 (mm) cc_final: 0.8094 (mt)
REVERT: C  204 MET cc_start: 0.6540 (ppp) cc_final: 0.6317 (mmp)
REVERT: C  267 PRO cc_start: 0.7234 (Cg_endo) cc_final: 0.6670 (Cg_exo)
REVERT: B   68 MET cc_start: 0.6615 (ttt) cc_final: 0.6306 (tmm)
REVERT: B   77 ASP cc_start: 0.7975 (m-30) cc_final: 0.7720 (m-30)
REVERT: B   83 ILE cc_start: 0.9073 (tp) cc_final: 0.8809 (tp)
REVERT: B  139 ASN cc_start: 0.5298 (t0) cc_final: 0.4668 (t0)
REVERT: B  166 MET cc_start: 0.7604 (tpp) cc_final: 0.7309 (tpp)
REVERT: D   53 PHE cc_start: 0.4582 (p90) cc_final: 0.4255 (p90)
REVERT: D  165 LEU cc_start: 0.7871 (mt) cc_final: 0.7420 (mt)
REVERT: D  171 MET cc_start: 0.5435 (ppp) cc_final: 0.4830 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.0620
  time to fit residues: 17.7319
Evaluate side-chains
  157 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 46 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 85 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 103 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0470
   chunk 95 optimal weight:    5.9990
   overall best weight:    0.6880

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

Flipped N/Q/H residues before XYZ refinement:
A   5 ASN
C 200 GLN
** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 250 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.172888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.154038 restraints weight = 19266.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.154626 restraints weight = 16034.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.156314 restraints weight = 12580.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.156585 restraints weight = 10186.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.156779 restraints weight = 9210.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.4107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6058
moved from start:          0.3513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8838  Z= 0.131
  Angle     :  0.628   7.302  11932  Z= 0.336
  Chirality :  0.044   0.200   1392
  Planarity :  0.004   0.064   1464
  Dihedral  :  4.751  33.250   1152
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  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: -0.00 (0.24), residues: 1070
  helix:  1.02 (0.20), residues: 609
  sheet:  0.59 (0.56), residues: 84
  loop : -1.88 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  27 
 TYR   0.017   0.002   TYR B 206 
 PHE   0.033   0.002   PHE A 143 
 TRP   0.013   0.001   TRP B 223 
 HIS   0.003   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8838)
  covalent geometry    : angle       0.62845 (11932)
  hydrogen bonds       : bond        0.03804 (  526)
  hydrogen bonds       : angle       4.63702 ( 1521)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A   29 SER cc_start: 0.6700 (t) cc_final: 0.6493 (t)
REVERT: C   20 ASP cc_start: 0.5472 (m-30) cc_final: 0.5043 (t0)
REVERT: C   27 ARG cc_start: 0.6563 (tpt-90) cc_final: 0.5673 (mmm-85)
REVERT: C  173 ILE cc_start: 0.7071 (mp) cc_final: 0.6816 (mp)
REVERT: C  242 ASP cc_start: 0.5871 (t0) cc_final: 0.4617 (m-30)
REVERT: C  267 PRO cc_start: 0.7230 (Cg_endo) cc_final: 0.6629 (Cg_exo)
REVERT: B   77 ASP cc_start: 0.8014 (m-30) cc_final: 0.7810 (m-30)
REVERT: B   83 ILE cc_start: 0.9135 (tp) cc_final: 0.8860 (tp)
REVERT: B  139 ASN cc_start: 0.5323 (t0) cc_final: 0.4802 (t0)
REVERT: B  166 MET cc_start: 0.7760 (tpp) cc_final: 0.7291 (tpp)
REVERT: D   53 PHE cc_start: 0.4669 (p90) cc_final: 0.4383 (p90)
REVERT: D  109 MET cc_start: 0.6002 (mmp) cc_final: 0.5800 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.0620
  time to fit residues: 17.7163
Evaluate side-chains
  150 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 102 optimal weight:    0.0020
   chunk 34 optimal weight:    0.0870
   chunk 55 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 46 optimal weight:    6.9990
   overall best weight:    0.5766

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

Flipped N/Q/H residues before XYZ refinement:
A   5 ASN
C 200 GLN
** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   5 ASN
** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 250 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.173168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.154557 restraints weight = 19283.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.155077 restraints weight = 16437.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.156258 restraints weight = 13345.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.156940 restraints weight = 10824.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.157039 restraints weight = 9544.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6044
moved from start:          0.3651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8838  Z= 0.127
  Angle     :  0.638   9.025  11932  Z= 0.339
  Chirality :  0.044   0.197   1392
  Planarity :  0.004   0.062   1464
  Dihedral  :  4.763  34.196   1152
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  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:  0.06 (0.24), residues: 1070
  helix:  1.10 (0.20), residues: 607
  sheet:  0.53 (0.53), residues: 87
  loop : -1.88 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  27 
 TYR   0.019   0.002   TYR B   9 
 PHE   0.033   0.002   PHE A 143 
 TRP   0.011   0.001   TRP B 223 
 HIS   0.003   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8838)
  covalent geometry    : angle       0.63849 (11932)
  hydrogen bonds       : bond        0.03773 (  526)
  hydrogen bonds       : angle       4.59994 ( 1521)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: C   20 ASP cc_start: 0.5613 (m-30) cc_final: 0.5118 (t0)
REVERT: C  242 ASP cc_start: 0.5964 (t0) cc_final: 0.4846 (m-30)
REVERT: C  267 PRO cc_start: 0.7233 (Cg_endo) cc_final: 0.6653 (Cg_exo)
REVERT: B   83 ILE cc_start: 0.9143 (tp) cc_final: 0.8851 (tp)
REVERT: B  139 ASN cc_start: 0.5334 (t0) cc_final: 0.4788 (t0)
REVERT: B  166 MET cc_start: 0.7741 (tpp) cc_final: 0.7286 (tpp)
REVERT: D   86 LEU cc_start: 0.5940 (tp) cc_final: 0.5564 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.0559
  time to fit residues: 15.7175
Evaluate side-chains
  154 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 19 optimal weight:    0.1980
   chunk 103 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0170
   chunk 61 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0040
   chunk 18 optimal weight:    0.0670
   chunk 25 optimal weight:    0.0980
   chunk 7 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0570
   overall best weight:    0.0486

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

Flipped N/Q/H residues before XYZ refinement:
A   5 ASN
C 200 GLN
** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   5 ASN
D 200 GLN
** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 250 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.175046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.156374 restraints weight = 19460.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.157903 restraints weight = 14993.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.158949 restraints weight = 12219.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.159714 restraints weight = 10460.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.160042 restraints weight = 9352.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.4149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5983
moved from start:          0.3701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8838  Z= 0.127
  Angle     :  0.634   9.097  11932  Z= 0.338
  Chirality :  0.044   0.200   1392
  Planarity :  0.004   0.065   1464
  Dihedral  :  4.691  33.859   1152
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  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:  0.15 (0.24), residues: 1070
  helix:  1.21 (0.20), residues: 608
  sheet:  0.49 (0.52), residues: 89
  loop : -1.91 (0.29), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 194 
 TYR   0.021   0.002   TYR A  51 
 PHE   0.034   0.002   PHE B 143 
 TRP   0.008   0.001   TRP B 223 
 HIS   0.003   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8838)
  covalent geometry    : angle       0.63424 (11932)
  hydrogen bonds       : bond        0.03606 (  526)
  hydrogen bonds       : angle       4.55698 ( 1521)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   29 SER cc_start: 0.6900 (t) cc_final: 0.6672 (t)
REVERT: A  123 GLN cc_start: 0.6386 (mm-40) cc_final: 0.5473 (mm-40)
REVERT: A  166 MET cc_start: 0.5239 (mmt) cc_final: 0.4328 (mtt)
REVERT: C   20 ASP cc_start: 0.5296 (m-30) cc_final: 0.4850 (t0)
REVERT: C   83 ASN cc_start: 0.6486 (m-40) cc_final: 0.6263 (m-40)
REVERT: C  150 MET cc_start: 0.6888 (ttp) cc_final: 0.6655 (ptm)
REVERT: C  242 ASP cc_start: 0.5733 (t0) cc_final: 0.4512 (m-30)
REVERT: C  267 PRO cc_start: 0.7177 (Cg_endo) cc_final: 0.6540 (Cg_exo)
REVERT: B   68 MET cc_start: 0.6257 (tmm) cc_final: 0.6028 (tmm)
REVERT: B  139 ASN cc_start: 0.5341 (t0) cc_final: 0.4912 (t0)
REVERT: B  166 MET cc_start: 0.7489 (tpp) cc_final: 0.7064 (tpp)
REVERT: B  182 LYS cc_start: 0.5029 (ttpt) cc_final: 0.4341 (mmtp)
REVERT: B  239 LEU cc_start: 0.5252 (mm) cc_final: 0.4965 (mt)
REVERT: D   63 ASP cc_start: 0.8084 (m-30) cc_final: 0.7884 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.0504
  time to fit residues: 15.2674
Evaluate side-chains
  154 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9990
   chunk 91 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 31 optimal weight:    0.4980
   chunk 85 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 95 optimal weight:    8.9990
   chunk 69 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 GLN
** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   5 ASN
D 200 GLN
D 234 GLN
D 250 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.170410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.151777 restraints weight = 19372.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.152275 restraints weight = 16079.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.152903 restraints weight = 13228.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.153418 restraints weight = 11677.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.153447 restraints weight = 10409.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.4062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6135
moved from start:          0.4056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8838  Z= 0.159
  Angle     :  0.681   9.140  11932  Z= 0.363
  Chirality :  0.046   0.232   1392
  Planarity :  0.004   0.066   1464
  Dihedral  :  4.855  34.898   1152
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  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: -0.14 (0.24), residues: 1070
  helix:  0.98 (0.20), residues: 611
  sheet:  0.30 (0.54), residues: 89
  loop : -2.06 (0.28), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  27 
 TYR   0.024   0.002   TYR A  51 
 PHE   0.036   0.002   PHE A 143 
 TRP   0.019   0.002   TRP A 221 
 HIS   0.005   0.001   HIS C   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 8838)
  covalent geometry    : angle       0.68146 (11932)
  hydrogen bonds       : bond        0.03984 (  526)
  hydrogen bonds       : angle       4.62073 ( 1521)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1031.42 seconds
wall clock time: 18 minutes 39.68 seconds (1119.68 seconds total)