Starting phenix.real_space_refine
on Tue Jan 13 14:13:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yso_34078/01_2026/7yso_34078.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yso_34078/01_2026/7yso_34078.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yso_34078/01_2026/7yso_34078.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yso_34078/01_2026/7yso_34078.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yso_34078/01_2026/7yso_34078.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yso_34078/01_2026/7yso_34078.map"
  }
  resolution = 3.6
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     S      48      5.16       5
     C    4278      2.51       5
     N    1162      2.21       5
     O    1317      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6810
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3374
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3374
          Classifications: {'peptide': 430}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3376
          Classifications: {'peptide': 430}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.79, per 1000 atoms: 0.26
  Number of scatterers: 6810
  At special positions: 0
  Unit cell: (111.28, 71.904, 67.624, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     P       5     15.00
     O    1317      8.00
     N    1162      7.00
     C    4278      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: 0.84
  Conformation dependent library (CDL) restraints added in 249.7 milliseconds
  

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1594

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      50.8% alpha, 13.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 28
    Processing helix  chain 'A' and resid 48 through 52
      removed outlier: 4.203A  pdb=" N   PHE A  52 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 48 through 52'
    Processing helix  chain 'A' and resid 72 through 80
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 111 through 127
      removed outlier: 4.295A  pdb=" N   ASP A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   LEU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 161
      removed outlier: 4.439A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 195
    Processing helix  chain 'A' and resid 206 through 216
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 4.911A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 259
    Processing helix  chain 'A' and resid 277 through 281
    Processing helix  chain 'A' and resid 287 through 296
      removed outlier: 4.304A  pdb=" N   PHE A 296 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 337
      removed outlier: 3.582A  pdb=" N   THR A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 400
      removed outlier: 4.022A  pdb=" N   TRP A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.861A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 436
      removed outlier: 3.933A  pdb=" N   PHE A 418 " --> pdb=" O   GLU A 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 28
    Processing helix  chain 'B' and resid 41 through 48
      removed outlier: 4.163A  pdb=" N   ARG B  48 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 71 through 81
      removed outlier: 3.815A  pdb=" N   MET B  75 " --> pdb=" O   GLU B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 92
    Processing helix  chain 'B' and resid 103 through 109
    Processing helix  chain 'B' and resid 111 through 129
      removed outlier: 3.585A  pdb=" N   ASP B 116 " --> pdb=" O   ALA B 112 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   SER B 117 " --> pdb=" O   GLU B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 161
    Processing helix  chain 'B' and resid 182 through 198
      removed outlier: 4.132A  pdb=" N   ASN B 186 " --> pdb=" O   VAL B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 216
    Processing helix  chain 'B' and resid 223 through 239
      removed outlier: 3.812A  pdb=" N   LEU B 230 " --> pdb=" O   ASP B 226 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   THR B 239 " --> pdb=" O   MET B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 243
    Processing helix  chain 'B' and resid 251 through 260
    Processing helix  chain 'B' and resid 287 through 295
      removed outlier: 3.601A  pdb=" N   LEU B 291 " --> pdb=" O   THR B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 310
    Processing helix  chain 'B' and resid 324 through 340
      removed outlier: 4.033A  pdb=" N   VAL B 328 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 343
      No H-bonds generated for 'chain 'B' and resid 341 through 343'
    Processing helix  chain 'B' and resid 384 through 400
      removed outlier: 3.843A  pdb=" N   PHE B 388 " --> pdb=" O   ILE B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 410
      removed outlier: 4.539A  pdb=" N   TYR B 408 " --> pdb=" O   PHE B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 437
      removed outlier: 3.812A  pdb=" N   PHE B 418 " --> pdb=" O   ASP B 414 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68
      removed outlier: 7.113A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   SER A 140 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 68
      removed outlier: 7.113A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   SER A 140 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 273
      removed outlier: 4.014A  pdb=" N   ASN A 380 " --> pdb=" O   ALA A 314 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   ALA A 314 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 67
      removed outlier: 8.694A  pdb=" N   ILE B  66 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   HIS B   6 " --> pdb=" O   ILE B  66 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   VAL B   5 " --> pdb=" O   GLN B 136 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   THR B 138 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ILE B   7 " --> pdb=" O   THR B 138 " (cutoff:3.500A)
      removed outlier: 8.744A  pdb=" N   SER B 140 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 5.531A  pdb=" N   PHE B 135 " --> pdb=" O   ASN B 167 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   PHE B 169 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   LEU B 137 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   VAL B 171 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 7.432A  pdb=" N   HIS B 139 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   GLU B 200 " --> pdb=" O   MET B 166 " (cutoff:3.500A)
      removed outlier: 7.977A  pdb=" N   ASP B 205 " --> pdb=" O   PRO B 270 " (cutoff:3.500A)
      removed outlier: 12.071A  pdb=" N   PHE B 272 " --> pdb=" O   ASP B 205 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   PHE B 267 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   SER B 381 " --> pdb=" O   PHE B 267 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLY B 379 " --> pdb=" O   MET B 269 " (cutoff:3.500A)
      removed outlier: 8.767A  pdb=" N   LYS B 352 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   VAL B 315 " --> pdb=" O   LYS B 352 " (cutoff:3.500A)
      removed outlier: 8.075A  pdb=" N   ALA B 354 " --> pdb=" O   VAL B 315 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ALA B 317 " --> pdb=" O   ALA B 354 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   CYS B 356 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   PHE B 319 " --> pdb=" O   CYS B 356 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 55

    330 hydrogen bonds defined for protein.
    960 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.00

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2274
        1.34 -     1.46: 1532
        1.46 -     1.58: 3073
        1.58 -     1.69: 11
        1.69 -     1.81: 76
  Bond restraints: 6966
  Sorted by residual:
  bond pdb=" C6  GTP A 501 "
       pdb=" O6  GTP A 501 "
    ideal  model  delta    sigma   weight residual
    1.230  1.463 -0.233 2.00e-02 2.50e+03 1.36e+02
  bond pdb=" C2' GTP A 501 "
       pdb=" C3' GTP A 501 "
    ideal  model  delta    sigma   weight residual
    1.524  1.332  0.192 2.00e-02 2.50e+03 9.17e+01
  bond pdb=" C3' GDP B 501 "
       pdb=" C2' GDP B 501 "
    ideal  model  delta    sigma   weight residual
    1.524  1.334  0.190 2.00e-02 2.50e+03 9.03e+01
  bond pdb=" C4' GDP B 501 "
       pdb=" O4' GDP B 501 "
    ideal  model  delta    sigma   weight residual
    1.426  1.600 -0.174 2.00e-02 2.50e+03 7.54e+01
  bond pdb=" C4' GTP A 501 "
       pdb=" O4' GTP A 501 "
    ideal  model  delta    sigma   weight residual
    1.410  1.566 -0.156 2.00e-02 2.50e+03 6.08e+01
  ... (remaining 6961 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 9305
        2.35 -     4.71: 122
        4.71 -     7.06: 23
        7.06 -     9.42: 11
        9.42 -    11.77: 1
  Bond angle restraints: 9462
  Sorted by residual:
  angle pdb=" N   VAL A 182 "
        pdb=" CA  VAL A 182 "
        pdb=" C   VAL A 182 "
      ideal   model   delta    sigma   weight residual
     112.29  107.43    4.86 9.40e-01 1.13e+00 2.67e+01
  angle pdb=" C   GLN A  35 "
        pdb=" N   MET A  36 "
        pdb=" CA  MET A  36 "
      ideal   model   delta    sigma   weight residual
     121.83  128.91   -7.08 1.56e+00 4.11e-01 2.06e+01
  angle pdb=" CB  MET B 235 "
        pdb=" CG  MET B 235 "
        pdb=" SD  MET B 235 "
      ideal   model   delta    sigma   weight residual
     112.70  124.47  -11.77 3.00e+00 1.11e-01 1.54e+01
  angle pdb=" N   SER B 324 "
        pdb=" CA  SER B 324 "
        pdb=" C   SER B 324 "
      ideal   model   delta    sigma   weight residual
     110.65  105.75    4.90 1.26e+00 6.30e-01 1.51e+01
  angle pdb=" CG  ARG B  79 "
        pdb=" CD  ARG B  79 "
        pdb=" NE  ARG B  79 "
      ideal   model   delta    sigma   weight residual
     112.00  103.76    8.24 2.20e+00 2.07e-01 1.40e+01
  ... (remaining 9457 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.56: 4044
       33.56 -    67.12: 84
       67.12 -   100.68: 14
      100.68 -   134.25: 1
      134.25 -   167.81: 1
  Dihedral angle restraints: 4144
    sinusoidal: 1659
      harmonic: 2485
  Sorted by residual:
  dihedral pdb=" C8  GTP A 501 "
           pdb=" C1' GTP A 501 "
           pdb=" N9  GTP A 501 "
           pdb=" O4' GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -87.60 -167.81     1      2.00e+01 2.50e-03 4.75e+01
  dihedral pdb=" C5' GTP A 501 "
           pdb=" O5' GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" O3A GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -164.21 -126.53     1      2.00e+01 2.50e-03 3.83e+01
  dihedral pdb=" CA  VAL B  93 "
           pdb=" C   VAL B  93 "
           pdb=" N   PHE B  94 "
           pdb=" CA  PHE B  94 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.98  -24.02     0      5.00e+00 4.00e-02 2.31e+01
  ... (remaining 4141 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 712
       0.041 -    0.082: 237
       0.082 -    0.122: 76
       0.122 -    0.163: 7
       0.163 -    0.204: 2
  Chirality restraints: 1034
  Sorted by residual:
  chirality pdb=" CB  THR B 221 "
            pdb=" CA  THR B 221 "
            pdb=" OG1 THR B 221 "
            pdb=" CG2 THR B 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" C4' GTP A 501 "
            pdb=" C3' GTP A 501 "
            pdb=" C5' GTP A 501 "
            pdb=" O4' GTP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.66    0.19 2.00e-01 2.50e+01 9.16e-01
  chirality pdb=" CA  GLU B 127 "
            pdb=" N   GLU B 127 "
            pdb=" C   GLU B 127 "
            pdb=" CB  GLU B 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.58e-01
  ... (remaining 1031 not shown)

  Planarity restraints: 1233
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  94 "    0.014 2.00e-02 2.50e+03   1.46e-02 3.75e+00
        pdb=" CG  PHE B  94 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  94 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  94 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  94 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  94 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  94 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 123 "   -0.009 2.00e-02 2.50e+03   1.71e-02 2.94e+00
        pdb=" C   ARG B 123 "    0.030 2.00e-02 2.50e+03
        pdb=" O   ARG B 123 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LYS B 124 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 297 "   -0.027 5.00e-02 4.00e+02   4.12e-02 2.71e+00
        pdb=" N   PRO A 298 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 298 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 298 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1230 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 780
        2.74 -     3.28: 7718
        3.28 -     3.82: 12458
        3.82 -     4.36: 14576
        4.36 -     4.90: 23901
  Nonbonded interactions: 59433
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 320 "
            pdb=" O   GLN A 358 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" NE2 GLN B  11 "
            pdb=" O2A GDP B 501 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" OG  SER A 241 "
            pdb=" O   VAL A 250 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OG  SER B 170 "
            pdb=" O   TYR B 202 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OH  TYR B 185 "
            pdb=" O   ALA B 403 "
     model   vdw
     2.278 3.040
  ... (remaining 59428 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.400
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
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      :  0.008   0.233   6966  Z= 0.394
  Angle     :  0.702  11.770   9462  Z= 0.348
  Chirality :  0.044   0.204   1034
  Planarity :  0.004   0.041   1233
  Dihedral  : 15.403 167.807   2550
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 19.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.12 (0.29), residues: 854
  helix:  0.49 (0.26), residues: 379
  sheet: -0.07 (0.47), residues: 130
  loop : -0.13 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 322 
 TYR   0.011   0.001   TYR A 432 
 PHE   0.033   0.002   PHE B  94 
 TRP   0.017   0.001   TRP B 103 
 HIS   0.003   0.001   HIS B  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00795 ( 6966)
  covalent geometry    : angle       0.70164 ( 9462)
  hydrogen bonds       : bond        0.15103 (  325)
  hydrogen bonds       : angle       7.01564 (  960)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 HIS cc_start: 0.8840 (m-70) cc_final: 0.8390 (m90)
REVERT: A  102 ASN cc_start: 0.9042 (t0) cc_final: 0.8264 (t0)
REVERT: B   76 ASP cc_start: 0.9031 (m-30) cc_final: 0.8549 (m-30)
REVERT: B  149 MET cc_start: 0.8699 (mmp) cc_final: 0.8162 (mmt)
REVERT: B  204 ILE cc_start: 0.7638 (mm) cc_final: 0.7406 (mm)
REVERT: B  329 ASP cc_start: 0.8832 (m-30) cc_final: 0.8582 (m-30)
REVERT: B  353 THR cc_start: 0.8106 (p) cc_final: 0.7678 (p)
REVERT: B  406 HIS cc_start: 0.9266 (m90) cc_final: 0.9056 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.0646
  time to fit residues: 13.0552
Evaluate side-chains
  111 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    8.9990
   overall best weight:    4.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 ASN
B 436 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.108360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.082694 restraints weight = 18787.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.086200 restraints weight = 10967.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.088745 restraints weight = 7640.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.090308 restraints weight = 5895.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.091583 restraints weight = 5007.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6966  Z= 0.238
  Angle     :  0.683   7.119   9462  Z= 0.357
  Chirality :  0.047   0.187   1034
  Planarity :  0.005   0.045   1233
  Dihedral  :  9.637 179.370    959
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 18.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  9.96 %
    Favored  : 88.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 (0.28), residues: 854
  helix:  0.20 (0.25), residues: 385
  sheet: -0.26 (0.45), residues: 122
  loop : -0.15 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 158 
 TYR   0.007   0.001   TYR A 103 
 PHE   0.025   0.002   PHE B  94 
 TRP   0.022   0.002   TRP B 103 
 HIS   0.007   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 ( 6966)
  covalent geometry    : angle       0.68325 ( 9462)
  hydrogen bonds       : bond        0.04638 (  325)
  hydrogen bonds       : angle       5.64203 (  960)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 127
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 ASP cc_start: 0.8679 (p0) cc_final: 0.8381 (p0)
REVERT: A   71 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7618 (tm-30)
REVERT: A  102 ASN cc_start: 0.9139 (t0) cc_final: 0.8468 (t0)
REVERT: A  238 ILE cc_start: 0.9309 (mt) cc_final: 0.9100 (mt)
REVERT: A  434 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8608 (pp20)
REVERT: B   92 PHE cc_start: 0.8815 (m-80) cc_final: 0.8599 (m-80)
REVERT: B  139 HIS cc_start: 0.8554 (p-80) cc_final: 0.8297 (p-80)
REVERT: B  149 MET cc_start: 0.8684 (mmp) cc_final: 0.8374 (mmt)
REVERT: B  166 MET cc_start: 0.8477 (tmm) cc_final: 0.7793 (tmm)
REVERT: B  235 MET cc_start: 0.8766 (tmm) cc_final: 0.8107 (tmm)
REVERT: B  301 MET cc_start: 0.9224 (tpp) cc_final: 0.8955 (tpp)
REVERT: B  329 ASP cc_start: 0.8886 (m-30) cc_final: 0.8637 (m-30)
REVERT: B  406 HIS cc_start: 0.9211 (m90) cc_final: 0.8994 (m90)
  outliers start: 8
  outliers final: 8
  residues processed: 129
  average time/residue: 0.0624
  time to fit residues: 11.8270
Evaluate side-chains
  119 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  387 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 79 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 53 optimal weight:   10.0000
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 82 optimal weight:    6.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 329 ASN
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.110000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.083832 restraints weight = 18328.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.087513 restraints weight = 10736.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.090056 restraints weight = 7480.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.091856 restraints weight = 5812.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.093084 restraints weight = 4853.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6966  Z= 0.170
  Angle     :  0.622   7.702   9462  Z= 0.321
  Chirality :  0.045   0.165   1034
  Planarity :  0.005   0.042   1233
  Dihedral  :  9.346 176.229    959
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 16.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.82 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.12 (0.28), residues: 854
  helix:  0.29 (0.25), residues: 383
  sheet: -0.42 (0.45), residues: 121
  loop : -0.17 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 158 
 TYR   0.007   0.001   TYR A 282 
 PHE   0.016   0.001   PHE A 255 
 TRP   0.025   0.002   TRP B 103 
 HIS   0.004   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 6966)
  covalent geometry    : angle       0.62233 ( 9462)
  hydrogen bonds       : bond        0.04090 (  325)
  hydrogen bonds       : angle       5.31030 (  960)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.7757 (tmm) cc_final: 0.7557 (tmm)
REVERT: A  102 ASN cc_start: 0.9096 (t0) cc_final: 0.8325 (t0)
REVERT: A  238 ILE cc_start: 0.9293 (mt) cc_final: 0.9068 (mt)
REVERT: B   75 MET cc_start: 0.8557 (ppp) cc_final: 0.8330 (ppp)
REVERT: B   94 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6546 (t80)
REVERT: B  139 HIS cc_start: 0.8528 (p-80) cc_final: 0.8190 (p-80)
REVERT: B  149 MET cc_start: 0.8706 (mmp) cc_final: 0.8426 (mmt)
REVERT: B  166 MET cc_start: 0.8447 (tmm) cc_final: 0.7705 (tmm)
REVERT: B  197 ASN cc_start: 0.8047 (t0) cc_final: 0.7756 (t0)
REVERT: B  210 TYR cc_start: 0.9078 (t80) cc_final: 0.8877 (t80)
REVERT: B  235 MET cc_start: 0.8697 (tmm) cc_final: 0.8028 (tmm)
REVERT: B  329 ASP cc_start: 0.8837 (m-30) cc_final: 0.8600 (m-30)
REVERT: B  353 THR cc_start: 0.8053 (p) cc_final: 0.7640 (p)
REVERT: B  406 HIS cc_start: 0.9213 (m90) cc_final: 0.8997 (m90)
  outliers start: 14
  outliers final: 8
  residues processed: 130
  average time/residue: 0.0626
  time to fit residues: 11.9449
Evaluate side-chains
  118 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  305 CYS
Chi-restraints excluded: chain B residue  387 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 82 optimal weight:    8.9990
   chunk 79 optimal weight:   20.0000
   chunk 37 optimal weight:    6.9990
   chunk 69 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    5.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.106008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.080235 restraints weight = 18895.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.083808 restraints weight = 10968.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.086369 restraints weight = 7640.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.088062 restraints weight = 5914.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.089257 restraints weight = 4968.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   6966  Z= 0.271
  Angle     :  0.681   8.626   9462  Z= 0.358
  Chirality :  0.047   0.175   1034
  Planarity :  0.005   0.049   1233
  Dihedral  :  9.441 173.818    959
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 20.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.55 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.39 (0.28), residues: 854
  helix:  0.09 (0.25), residues: 388
  sheet: -0.81 (0.47), residues: 115
  loop : -0.26 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 158 
 TYR   0.010   0.001   TYR A 103 
 PHE   0.017   0.002   PHE A 169 
 TRP   0.027   0.002   TRP B 103 
 HIS   0.005   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 ( 6966)
  covalent geometry    : angle       0.68150 ( 9462)
  hydrogen bonds       : bond        0.04563 (  325)
  hydrogen bonds       : angle       5.40543 (  960)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.7769 (tmm) cc_final: 0.7560 (tmm)
REVERT: A  102 ASN cc_start: 0.9224 (t0) cc_final: 0.8583 (t0)
REVERT: A  238 ILE cc_start: 0.9356 (mt) cc_final: 0.9130 (mt)
REVERT: B   75 MET cc_start: 0.8756 (ppp) cc_final: 0.8503 (ppp)
REVERT: B   76 ASP cc_start: 0.8996 (m-30) cc_final: 0.8442 (m-30)
REVERT: B   94 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.6342 (t80)
REVERT: B  139 HIS cc_start: 0.8605 (p-80) cc_final: 0.8258 (p-80)
REVERT: B  149 MET cc_start: 0.8811 (mmp) cc_final: 0.8583 (mmt)
REVERT: B  166 MET cc_start: 0.8442 (tmm) cc_final: 0.7672 (tmm)
REVERT: B  235 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8203 (tmm)
REVERT: B  329 ASP cc_start: 0.8834 (m-30) cc_final: 0.8608 (m-30)
REVERT: B  332 MET cc_start: 0.8972 (mmp) cc_final: 0.8772 (mmp)
REVERT: B  416 MET cc_start: 0.9691 (ppp) cc_final: 0.9432 (ppp)
  outliers start: 23
  outliers final: 13
  residues processed: 128
  average time/residue: 0.0653
  time to fit residues: 12.2302
Evaluate side-chains
  122 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue   16 ILE
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  305 CYS
Chi-restraints excluded: chain B residue  387 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 78 optimal weight:   20.0000
   chunk 37 optimal weight:    0.0980
   chunk 20 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 32 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 57 optimal weight:   20.0000
   chunk 31 optimal weight:    8.9990
   chunk 81 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   overall best weight:    1.8188

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

Flipped N/Q/H residues before XYZ refinement:
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 426 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.110248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.084094 restraints weight = 18214.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.087799 restraints weight = 10739.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.090359 restraints weight = 7518.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.092147 restraints weight = 5851.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.093379 restraints weight = 4903.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6966  Z= 0.140
  Angle     :  0.649   9.206   9462  Z= 0.325
  Chirality :  0.045   0.164   1034
  Planarity :  0.005   0.042   1233
  Dihedral  :  9.161 170.642    959
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.46 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.31 (0.28), residues: 854
  helix:  0.16 (0.25), residues: 388
  sheet: -0.61 (0.49), residues: 108
  loop : -0.29 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  79 
 TYR   0.016   0.001   TYR B 210 
 PHE   0.014   0.002   PHE B 388 
 TRP   0.027   0.002   TRP B 103 
 HIS   0.004   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6966)
  covalent geometry    : angle       0.64908 ( 9462)
  hydrogen bonds       : bond        0.03866 (  325)
  hydrogen bonds       : angle       5.04506 (  960)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.7746 (tmm) cc_final: 0.7525 (tmm)
REVERT: A  102 ASN cc_start: 0.9078 (t0) cc_final: 0.8339 (t0)
REVERT: A  238 ILE cc_start: 0.9316 (mt) cc_final: 0.9083 (mt)
REVERT: B   75 MET cc_start: 0.8899 (ppp) cc_final: 0.8361 (ppp)
REVERT: B   79 ARG cc_start: 0.8786 (mtm180) cc_final: 0.8383 (tpm170)
REVERT: B   94 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6514 (t80)
REVERT: B  149 MET cc_start: 0.8717 (mmp) cc_final: 0.8472 (mmt)
REVERT: B  166 MET cc_start: 0.8492 (tmm) cc_final: 0.7675 (tmm)
REVERT: B  235 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8134 (tmm)
REVERT: B  272 PHE cc_start: 0.8999 (t80) cc_final: 0.8568 (t80)
REVERT: B  325 MET cc_start: 0.8577 (ppp) cc_final: 0.7827 (ppp)
REVERT: B  329 ASP cc_start: 0.8802 (m-30) cc_final: 0.8466 (m-30)
REVERT: B  416 MET cc_start: 0.9680 (ppp) cc_final: 0.9422 (ppp)
  outliers start: 18
  outliers final: 13
  residues processed: 130
  average time/residue: 0.0630
  time to fit residues: 11.9647
Evaluate side-chains
  135 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  305 CYS
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  406 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 8 optimal weight:    0.0370
   chunk 9 optimal weight:   10.0000
   chunk 7 optimal weight:    0.3980
   chunk 1 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 81 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 71 optimal weight:    0.0470
   chunk 53 optimal weight:    7.9990
   overall best weight:    0.4556

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

Flipped N/Q/H residues before XYZ refinement:
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.113617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.087249 restraints weight = 17600.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.091033 restraints weight = 10359.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.093678 restraints weight = 7211.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.095537 restraints weight = 5584.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.096840 restraints weight = 4647.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6966  Z= 0.115
  Angle     :  0.659   8.821   9462  Z= 0.324
  Chirality :  0.045   0.201   1034
  Planarity :  0.004   0.042   1233
  Dihedral  :  8.790 162.501    959
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.51 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.22 (0.28), residues: 854
  helix:  0.28 (0.25), residues: 389
  sheet: -0.49 (0.49), residues: 111
  loop : -0.32 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 369 
 TYR   0.011   0.001   TYR A 224 
 PHE   0.021   0.001   PHE A 135 
 TRP   0.031   0.002   TRP B 103 
 HIS   0.003   0.001   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6966)
  covalent geometry    : angle       0.65881 ( 9462)
  hydrogen bonds       : bond        0.03571 (  325)
  hydrogen bonds       : angle       4.81577 (  960)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 138
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.7698 (tmm) cc_final: 0.7472 (tmm)
REVERT: A  102 ASN cc_start: 0.8996 (t0) cc_final: 0.8233 (t0)
REVERT: A  386 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7730 (tm-30)
REVERT: B   75 MET cc_start: 0.8847 (ppp) cc_final: 0.8613 (ppp)
REVERT: B   94 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.6534 (t80)
REVERT: B  135 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7507 (m-80)
REVERT: B  139 HIS cc_start: 0.8656 (p-80) cc_final: 0.8297 (p-80)
REVERT: B  149 MET cc_start: 0.8590 (mmp) cc_final: 0.8199 (mmp)
REVERT: B  166 MET cc_start: 0.8487 (tmm) cc_final: 0.7604 (tmm)
REVERT: B  185 TYR cc_start: 0.8388 (m-80) cc_final: 0.8117 (m-80)
REVERT: B  235 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8086 (tmm)
REVERT: B  272 PHE cc_start: 0.8991 (t80) cc_final: 0.8566 (t80)
REVERT: B  329 ASP cc_start: 0.8820 (m-30) cc_final: 0.8593 (m-30)
REVERT: B  416 MET cc_start: 0.9674 (ppp) cc_final: 0.9422 (ppp)
  outliers start: 17
  outliers final: 11
  residues processed: 144
  average time/residue: 0.0616
  time to fit residues: 12.7593
Evaluate side-chains
  135 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  135 PHE
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  305 CYS
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  406 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 50 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 30 optimal weight:    8.9990
   chunk 37 optimal weight:   10.0000
   chunk 40 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 43 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 380 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.106388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.080250 restraints weight = 18759.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.083879 restraints weight = 11016.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.086397 restraints weight = 7734.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.088032 restraints weight = 6047.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.089342 restraints weight = 5125.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   6966  Z= 0.298
  Angle     :  0.732   9.088   9462  Z= 0.381
  Chirality :  0.048   0.244   1034
  Planarity :  0.005   0.047   1233
  Dihedral  :  9.179 164.370    959
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 20.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 20.60 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.52 (0.28), residues: 854
  helix:  0.06 (0.25), residues: 388
  sheet: -1.41 (0.46), residues: 109
  loop : -0.23 (0.34), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  48 
 TYR   0.047   0.002   TYR A 224 
 PHE   0.020   0.002   PHE A 169 
 TRP   0.029   0.002   TRP B 103 
 HIS   0.007   0.002   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00621 ( 6966)
  covalent geometry    : angle       0.73231 ( 9462)
  hydrogen bonds       : bond        0.04446 (  325)
  hydrogen bonds       : angle       5.21687 (  960)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.7171 (tt0) cc_final: 0.6452 (tp30)
REVERT: A  102 ASN cc_start: 0.9257 (t0) cc_final: 0.8633 (t0)
REVERT: A  346 TRP cc_start: 0.8583 (p-90) cc_final: 0.8345 (p-90)
REVERT: A  386 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8002 (tm-30)
REVERT: B   26 ASP cc_start: 0.8895 (t70) cc_final: 0.8629 (t70)
REVERT: B   28 HIS cc_start: 0.9015 (OUTLIER) cc_final: 0.8785 (m-70)
REVERT: B   47 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8784 (tm-30)
REVERT: B   75 MET cc_start: 0.8934 (ppp) cc_final: 0.8335 (ppp)
REVERT: B   79 ARG cc_start: 0.8759 (mtm180) cc_final: 0.8296 (tpm170)
REVERT: B   94 PHE cc_start: 0.6702 (OUTLIER) cc_final: 0.6342 (t80)
REVERT: B  139 HIS cc_start: 0.8772 (p-80) cc_final: 0.8380 (p-80)
REVERT: B  149 MET cc_start: 0.8836 (mmp) cc_final: 0.8420 (mmp)
REVERT: B  235 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8439 (tmm)
REVERT: B  329 ASP cc_start: 0.8852 (m-30) cc_final: 0.8401 (m-30)
REVERT: B  380 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7694 (m-40)
  outliers start: 27
  outliers final: 15
  residues processed: 138
  average time/residue: 0.0653
  time to fit residues: 12.8844
Evaluate side-chains
  139 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue   28 HIS
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  305 CYS
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  406 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 81 optimal weight:    9.9990
   chunk 48 optimal weight:    6.9990
   chunk 8 optimal weight:    0.0000
   chunk 85 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:   20.0000
   chunk 39 optimal weight:    2.9990
   chunk 84 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 79 optimal weight:    6.9990
   overall best weight:    2.7992

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

Flipped N/Q/H residues before XYZ refinement:
B 380 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.110392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.086733 restraints weight = 18623.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.090316 restraints weight = 10894.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.092998 restraints weight = 7522.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.094682 restraints weight = 5702.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.096036 restraints weight = 4724.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6966  Z= 0.174
  Angle     :  0.734   9.963   9462  Z= 0.364
  Chirality :  0.047   0.242   1034
  Planarity :  0.005   0.059   1233
  Dihedral  :  9.087 163.668    959
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 18.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 21.56 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.46 (0.28), residues: 854
  helix:  0.12 (0.25), residues: 388
  sheet: -1.29 (0.49), residues: 108
  loop : -0.24 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  79 
 TYR   0.029   0.001   TYR A 224 
 PHE   0.015   0.002   PHE A 135 
 TRP   0.033   0.002   TRP B 103 
 HIS   0.003   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 6966)
  covalent geometry    : angle       0.73415 ( 9462)
  hydrogen bonds       : bond        0.04007 (  325)
  hydrogen bonds       : angle       5.09228 (  960)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9155 (t0) cc_final: 0.8455 (t0)
REVERT: A  250 VAL cc_start: 0.6191 (OUTLIER) cc_final: 0.5913 (p)
REVERT: A  346 TRP cc_start: 0.8579 (p-90) cc_final: 0.8349 (p-90)
REVERT: A  386 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7788 (tm-30)
REVERT: B   26 ASP cc_start: 0.8734 (t70) cc_final: 0.8518 (t70)
REVERT: B   47 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8648 (tm-30)
REVERT: B   75 MET cc_start: 0.8969 (ppp) cc_final: 0.8392 (ppp)
REVERT: B   79 ARG cc_start: 0.8726 (mtm180) cc_final: 0.8244 (tpm170)
REVERT: B   94 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6582 (t80)
REVERT: B  135 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7625 (m-80)
REVERT: B  139 HIS cc_start: 0.8711 (p-80) cc_final: 0.8391 (p-80)
REVERT: B  149 MET cc_start: 0.8691 (mmp) cc_final: 0.8337 (mmp)
REVERT: B  166 MET cc_start: 0.8441 (tmm) cc_final: 0.7389 (tmm)
REVERT: B  235 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8291 (tmm)
REVERT: B  272 PHE cc_start: 0.8987 (t80) cc_final: 0.8437 (t80)
REVERT: B  301 MET cc_start: 0.9269 (tpp) cc_final: 0.8588 (mmm)
REVERT: B  329 ASP cc_start: 0.8713 (m-30) cc_final: 0.8452 (m-30)
REVERT: B  388 PHE cc_start: 0.8023 (m-80) cc_final: 0.7749 (m-80)
  outliers start: 24
  outliers final: 16
  residues processed: 134
  average time/residue: 0.0623
  time to fit residues: 12.0485
Evaluate side-chains
  141 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  135 PHE
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  305 CYS
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  406 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 55 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 50 optimal weight:    8.9990
   chunk 64 optimal weight:    7.9990
   chunk 35 optimal weight:    0.0040
   chunk 78 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    1.0794

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

Flipped N/Q/H residues before XYZ refinement:
B 380 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.112083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.085584 restraints weight = 17935.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.089247 restraints weight = 10562.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.091839 restraints weight = 7393.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.093701 restraints weight = 5750.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.094894 restraints weight = 4798.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6966  Z= 0.130
  Angle     :  0.731  11.133   9462  Z= 0.356
  Chirality :  0.046   0.244   1034
  Planarity :  0.005   0.063   1233
  Dihedral  :  8.860 163.708    959
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 21.96 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.35 (0.28), residues: 854
  helix:  0.27 (0.25), residues: 388
  sheet: -1.14 (0.50), residues: 112
  loop : -0.29 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  79 
 TYR   0.023   0.001   TYR A 224 
 PHE   0.015   0.001   PHE A 135 
 TRP   0.032   0.002   TRP B 103 
 HIS   0.008   0.001   HIS B  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6966)
  covalent geometry    : angle       0.73144 ( 9462)
  hydrogen bonds       : bond        0.03681 (  325)
  hydrogen bonds       : angle       4.88024 (  960)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9023 (t0) cc_final: 0.8282 (t0)
REVERT: A  250 VAL cc_start: 0.6056 (OUTLIER) cc_final: 0.5822 (p)
REVERT: A  346 TRP cc_start: 0.8646 (p-90) cc_final: 0.8413 (p-90)
REVERT: A  386 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7839 (tm-30)
REVERT: B   26 ASP cc_start: 0.8694 (t70) cc_final: 0.8460 (t70)
REVERT: B   47 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8705 (tm-30)
REVERT: B   75 MET cc_start: 0.8987 (ppp) cc_final: 0.8680 (ppp)
REVERT: B   94 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.6409 (t80)
REVERT: B  135 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7746 (m-80)
REVERT: B  139 HIS cc_start: 0.8673 (p-80) cc_final: 0.8254 (p-80)
REVERT: B  149 MET cc_start: 0.8644 (mmp) cc_final: 0.8246 (mmp)
REVERT: B  185 TYR cc_start: 0.8385 (m-80) cc_final: 0.8087 (m-80)
REVERT: B  235 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8234 (tmm)
REVERT: B  272 PHE cc_start: 0.9008 (t80) cc_final: 0.8475 (t80)
REVERT: B  329 ASP cc_start: 0.8799 (m-30) cc_final: 0.8497 (m-30)
  outliers start: 21
  outliers final: 15
  residues processed: 139
  average time/residue: 0.0646
  time to fit residues: 13.0890
Evaluate side-chains
  143 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  135 PHE
Chi-restraints excluded: chain B residue  186 ASN
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  305 CYS
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  406 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 57 optimal weight:   30.0000
   chunk 14 optimal weight:    1.9990
   chunk 68 optimal weight:    0.4980
   chunk 81 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 60 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 42 optimal weight:   10.0000
   overall best weight:    1.6988

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

Flipped N/Q/H residues before XYZ refinement:
** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.111919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.087957 restraints weight = 17883.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.091584 restraints weight = 10567.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.094185 restraints weight = 7279.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.096016 restraints weight = 5537.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.097240 restraints weight = 4538.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6966  Z= 0.139
  Angle     :  0.735  10.685   9462  Z= 0.358
  Chirality :  0.046   0.249   1034
  Planarity :  0.004   0.057   1233
  Dihedral  :  8.737 163.211    959
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 21.83 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.28), residues: 854
  helix:  0.33 (0.25), residues: 386
  sheet: -1.16 (0.50), residues: 108
  loop : -0.22 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  79 
 TYR   0.021   0.001   TYR A 224 
 PHE   0.011   0.001   PHE B 377 
 TRP   0.035   0.002   TRP B 103 
 HIS   0.007   0.001   HIS B  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6966)
  covalent geometry    : angle       0.73527 ( 9462)
  hydrogen bonds       : bond        0.03690 (  325)
  hydrogen bonds       : angle       4.84305 (  960)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9088 (t0) cc_final: 0.8337 (t0)
REVERT: A  250 VAL cc_start: 0.6218 (OUTLIER) cc_final: 0.5947 (p)
REVERT: A  346 TRP cc_start: 0.8663 (p-90) cc_final: 0.8427 (p-90)
REVERT: A  386 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7809 (tm-30)
REVERT: B   26 ASP cc_start: 0.8696 (t70) cc_final: 0.8471 (t70)
REVERT: B   47 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8693 (tm-30)
REVERT: B   75 MET cc_start: 0.8972 (ppp) cc_final: 0.8400 (ppp)
REVERT: B   79 ARG cc_start: 0.8743 (mtm180) cc_final: 0.8227 (tpm170)
REVERT: B   94 PHE cc_start: 0.6927 (OUTLIER) cc_final: 0.6564 (t80)
REVERT: B  139 HIS cc_start: 0.8647 (p-80) cc_final: 0.8233 (p-80)
REVERT: B  149 MET cc_start: 0.8555 (mmp) cc_final: 0.8173 (mmp)
REVERT: B  235 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8318 (tmm)
REVERT: B  272 PHE cc_start: 0.9010 (t80) cc_final: 0.8591 (t80)
REVERT: B  275 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6923 (pp)
REVERT: B  329 ASP cc_start: 0.8771 (m-30) cc_final: 0.8497 (m-30)
  outliers start: 17
  outliers final: 12
  residues processed: 133
  average time/residue: 0.0626
  time to fit residues: 12.0738
Evaluate side-chains
  142 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  305 CYS
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  406 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 81 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 229 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.111443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.087299 restraints weight = 18161.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.090872 restraints weight = 10644.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.093239 restraints weight = 7358.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.095160 restraints weight = 5725.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.096296 restraints weight = 4701.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.2714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6966  Z= 0.152
  Angle     :  0.742  10.956   9462  Z= 0.361
  Chirality :  0.046   0.228   1034
  Planarity :  0.005   0.059   1233
  Dihedral  :  8.699 162.613    959
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 16.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 22.37 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.25 (0.28), residues: 854
  helix:  0.36 (0.25), residues: 386
  sheet: -1.13 (0.50), residues: 108
  loop : -0.25 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  79 
 TYR   0.021   0.001   TYR A 224 
 PHE   0.011   0.001   PHE B  92 
 TRP   0.034   0.002   TRP B 103 
 HIS   0.006   0.001   HIS B  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 6966)
  covalent geometry    : angle       0.74151 ( 9462)
  hydrogen bonds       : bond        0.03698 (  325)
  hydrogen bonds       : angle       4.85469 (  960)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1274.77 seconds
wall clock time: 22 minutes 53.89 seconds (1373.89 seconds total)