Starting phenix.real_space_refine
on Thu Jul  2 09:55:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/11hu_75703/07_2026/11hu_75703.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/11hu_75703/07_2026/11hu_75703.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/11hu_75703/07_2026/11hu_75703.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/11hu_75703/07_2026/11hu_75703.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/11hu_75703/07_2026/11hu_75703.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/11hu_75703/07_2026/11hu_75703.map"
  }
  resolution = 2.9
  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=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     192      5.49       5
     Mg      2      5.21       5
     S      23      5.16       5
     C    4327      2.51       5
     N    1525      2.21       5
     O    2018      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8088
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3980
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 495, 3980
          Classifications: {'peptide': 495}
          Link IDs: {'PTRANS': 21, 'TRANS': 473}
    Chain: "D"
      Number of atoms: 179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 179
          Classifications: {'DNA': 9}
          Link IDs: {'rna3p': 8}
    Chain: "B"
      Number of atoms: 3926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 3926
          Classifications: {'RNA': 183}
          Modifications used: {'rna2p_pur': 20, 'rna2p_pyr': 13, 'rna3p_pur': 87, 'rna3p_pyr': 63}
          Link IDs: {'rna2p': 32, 'rna3p': 150}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 2, ' ZN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1879  SG  CYS A 234      74.814  15.058  66.994  1.00248.14           S
  ATOM   1904  SG  CYS A 237      78.071  13.701  68.506  1.00248.22           S
  ATOM   2132  SG  CYS A 265      75.485  11.412  66.886  1.00244.98           S

  Time building chain proxies: 1.71, per 1000 atoms: 0.21
  Number of scatterers: 8088
  At special positions: 0
  Unit cell: (89.1, 116.325, 125.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      23     16.00
     P     192     15.00
     Mg      2     11.99
     O    2018      8.00
     N    1525      7.00
     C    4327      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: 0.76
  Conformation dependent library (CDL) restraints added in 281.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 503 "
        pdb="ZN    ZN A 503 " - pdb=" ND1 HIS A 268 "
        pdb="ZN    ZN A 503 " - pdb=" SG  CYS A 234 "
        pdb="ZN    ZN A 503 " - pdb=" SG  CYS A 265 "
        pdb="ZN    ZN A 503 " - pdb=" SG  CYS A 237 "
      Number of angles added : 3


  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  924

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 6 sheets defined
      36.2% alpha, 15.8% beta
      64 base pairs and 99 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 29
    Processing helix  chain 'A' and resid 88 through 108
      removed outlier: 4.466A  pdb=" N   LYS A  92 " --> pdb=" O   LYS A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 121
    Processing helix  chain 'A' and resid 163 through 182
    Processing helix  chain 'A' and resid 194 through 199
    Processing helix  chain 'A' and resid 221 through 230
    Processing helix  chain 'A' and resid 249 through 253
    Processing helix  chain 'A' and resid 257 through 259
      No H-bonds generated for 'chain 'A' and resid 257 through 259'
    Processing helix  chain 'A' and resid 265 through 275
    Processing helix  chain 'A' and resid 275 through 293
    Processing helix  chain 'A' and resid 302 through 314
    Processing helix  chain 'A' and resid 323 through 334
    Processing helix  chain 'A' and resid 338 through 340
      No H-bonds generated for 'chain 'A' and resid 338 through 340'
    Processing helix  chain 'A' and resid 341 through 350
      removed outlier: 3.998A  pdb=" N   ALA A 350 " --> pdb=" O   ILE A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 416
    Processing helix  chain 'A' and resid 417 through 424
      removed outlier: 3.521A  pdb=" N   VAL A 421 " --> pdb=" O   SER A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 465
      removed outlier: 3.529A  pdb=" N   GLY A 464 " --> pdb=" O   ARG A 461 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7
      removed outlier: 6.319A  pdb=" N   TYR A   5 " --> pdb=" O   ILE A  42 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   LEU A  44 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   ILE A   7 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 208
      removed outlier: 6.939A  pdb=" N   GLN A 207 " --> pdb=" O   VAL A 320 " (cutoff:3.500A)
      removed outlier: 9.217A  pdb=" N   SER A 322 " --> pdb=" O   GLN A 207 " (cutoff:3.500A)
      removed outlier: 5.948A  pdb=" N   LEU A  55 " --> pdb=" O   VAL A 186 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   THR A  72 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   SER A  77 " --> pdb=" O   THR A  72 " (cutoff:3.500A)
      removed outlier: 9.084A  pdb=" N   TYR A 365 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   ASN A  80 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   VAL A 367 " --> pdb=" O   ASN A  80 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   GLN A  82 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   GLN A 369 " --> pdb=" O   GLN A  82 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   GLU A  84 " --> pdb=" O   GLN A 369 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 131
    Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 246
    Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 393
    Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 478
      removed outlier: 6.537A  pdb=" N   VAL A 446 " --> pdb=" O   TYR A 484 " (cutoff:3.500A)
      removed outlier: 5.761A  pdb=" N   TYR A 484 " --> pdb=" O   VAL A 446 " (cutoff:3.500A)

    160 hydrogen bonds defined for protein.
    453 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      166 hydrogen bonds
      304 hydrogen bond angles
      0 basepair planarities
      64 basepair parallelities
      99 stacking parallelities
  Total time for adding SS restraints: 1.32

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1875
        1.34 -     1.46: 2870
        1.46 -     1.58: 3492
        1.58 -     1.70: 381
        1.70 -     1.82: 37
  Bond restraints: 8655
  Sorted by residual:
  bond pdb=" N9    A B  34 "
       pdb=" C4    A B  34 "
    ideal  model  delta    sigma   weight residual
    1.374  1.387 -0.013 6.00e-03 2.78e+04 4.76e+00
  bond pdb=" C3'  DT D   7 "
       pdb=" O3'  DT D   7 "
    ideal  model  delta    sigma   weight residual
    1.435  1.410  0.025 1.30e-02 5.92e+03 3.72e+00
  bond pdb=" C4'  DG D   5 "
       pdb=" C3'  DG D   5 "
    ideal  model  delta    sigma   weight residual
    1.529  1.510  0.019 1.00e-02 1.00e+04 3.48e+00
  bond pdb=" C4'  DT D   3 "
       pdb=" C3'  DT D   3 "
    ideal  model  delta    sigma   weight residual
    1.529  1.510  0.019 1.00e-02 1.00e+04 3.46e+00
  bond pdb=" C3'  DC D   8 "
       pdb=" O3'  DC D   8 "
    ideal  model  delta    sigma   weight residual
    1.435  1.412  0.023 1.30e-02 5.92e+03 3.02e+00
  ... (remaining 8650 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 12333
        1.46 -     2.92: 228
        2.92 -     4.38: 37
        4.38 -     5.83: 5
        5.83 -     7.29: 1
  Bond angle restraints: 12604
  Sorted by residual:
  angle pdb=" O2    C B 219 "
        pdb=" C2    C B 219 "
        pdb=" N3    C B 219 "
      ideal   model   delta    sigma   weight residual
     121.90  118.11    3.79 7.00e-01 2.04e+00 2.94e+01
  angle pdb=" C1'   C B  88 "
        pdb=" N1    C B  88 "
        pdb=" C2    C B  88 "
      ideal   model   delta    sigma   weight residual
     118.80  124.25   -5.45 1.10e+00 8.26e-01 2.45e+01
  angle pdb=" O2    C B  49 "
        pdb=" C2    C B  49 "
        pdb=" N3    C B  49 "
      ideal   model   delta    sigma   weight residual
     121.90  118.78    3.12 7.00e-01 2.04e+00 1.99e+01
  angle pdb=" O4'  DT D   3 "
        pdb=" C4'  DT D   3 "
        pdb=" C3'  DT D   3 "
      ideal   model   delta    sigma   weight residual
     106.00  103.49    2.51 6.00e-01 2.78e+00 1.75e+01
  angle pdb=" N3   DT D   6 "
        pdb=" C4   DT D   6 "
        pdb=" O4   DT D   6 "
      ideal   model   delta    sigma   weight residual
     119.90  122.39   -2.49 6.00e-01 2.78e+00 1.72e+01
  ... (remaining 12599 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.73: 4938
       35.73 -    71.47: 410
       71.47 -   107.20: 52
      107.20 -   142.94: 3
      142.94 -   178.67: 6
  Dihedral angle restraints: 5409
    sinusoidal: 3972
      harmonic: 1437
  Sorted by residual:
  dihedral pdb=" O4'   C B  49 "
           pdb=" C1'   C B  49 "
           pdb=" N1    C B  49 "
           pdb=" C2    C B  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   47.12  152.88     1      1.50e+01 4.44e-03 8.06e+01
  dihedral pdb=" O4'   U B 229 "
           pdb=" C1'   U B 229 "
           pdb=" N1    U B 229 "
           pdb=" C2    U B 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   53.33  178.67     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   C B  83 "
           pdb=" C1'   C B  83 "
           pdb=" N1    C B  83 "
           pdb=" C2    C B  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   49.79 -177.79     1      1.70e+01 3.46e-03 6.64e+01
  ... (remaining 5406 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1431
       0.061 -    0.123: 86
       0.123 -    0.184: 10
       0.184 -    0.246: 0
       0.246 -    0.307: 1
  Chirality restraints: 1528
  Sorted by residual:
  chirality pdb=" CB  ILE A 145 "
            pdb=" CA  ILE A 145 "
            pdb=" CG1 ILE A 145 "
            pdb=" CG2 ILE A 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" C3'   A B  86 "
            pdb=" C4'   A B  86 "
            pdb=" O3'   A B  86 "
            pdb=" C2'   A B  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.30   -0.18 2.00e-01 2.50e+01 8.31e-01
  chirality pdb=" C1'   G B   7 "
            pdb=" O4'   G B   7 "
            pdb=" C2'   G B   7 "
            pdb=" N9    G B   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.28    0.18 2.00e-01 2.50e+01 7.89e-01
  ... (remaining 1525 not shown)

  Planarity restraints: 897
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B 219 "    0.008 2.00e-02 2.50e+03   1.96e-02 8.64e+00
        pdb=" N1    C B 219 "   -0.005 2.00e-02 2.50e+03
        pdb=" C2    C B 219 "   -0.049 2.00e-02 2.50e+03
        pdb=" O2    C B 219 "    0.026 2.00e-02 2.50e+03
        pdb=" N3    C B 219 "    0.009 2.00e-02 2.50e+03
        pdb=" C4    C B 219 "   -0.010 2.00e-02 2.50e+03
        pdb=" N4    C B 219 "    0.009 2.00e-02 2.50e+03
        pdb=" C5    C B 219 "    0.005 2.00e-02 2.50e+03
        pdb=" C6    C B 219 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 163 "   -0.035 5.00e-02 4.00e+02   5.36e-02 4.60e+00
        pdb=" N   PRO A 164 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 164 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 164 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  80 "    0.028 2.00e-02 2.50e+03   1.22e-02 4.44e+00
        pdb=" N9    G B  80 "   -0.029 2.00e-02 2.50e+03
        pdb=" C8    G B  80 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    G B  80 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G B  80 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    G B  80 "   -0.001 2.00e-02 2.50e+03
        pdb=" O6    G B  80 "    0.010 2.00e-02 2.50e+03
        pdb=" N1    G B  80 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    G B  80 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G B  80 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    G B  80 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    G B  80 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 894 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 201
        2.66 -     3.22: 7153
        3.22 -     3.78: 15843
        3.78 -     4.34: 20154
        4.34 -     4.90: 28023
  Nonbonded interactions: 71374
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS A 245 "
            pdb="MG    MG A 502 "
     model   vdw
     2.103 2.250
  nonbonded pdb=" OD1 ASP A  60 "
            pdb="MG    MG A 501 "
     model   vdw
     2.105 2.170
  nonbonded pdb=" NE2 HIS A 269 "
            pdb="MG    MG A 502 "
     model   vdw
     2.125 2.250
  nonbonded pdb=" NE2 HIS A 273 "
            pdb="MG    MG A 502 "
     model   vdw
     2.213 2.250
  nonbonded pdb=" SG  CYS A 237 "
            pdb=" CE1 HIS A 268 "
     model   vdw
     2.442 2.896
  ... (remaining 71369 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.660
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.330
  Find NCS groups from input model:        0.030
  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:6.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8659  Z= 0.209
  Angle     :  0.506   7.293  12607  Z= 0.419
  Chirality :  0.033   0.307   1528
  Planarity :  0.004   0.054    897
  Dihedral  : 21.609 178.670   4485
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.40), residues: 493
  helix:  1.78 (0.41), residues: 168
  sheet: -0.47 (0.66), residues: 78
  loop :  0.05 (0.41), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 270 
 TYR   0.008   0.001   TYR A   5 
 PHE   0.014   0.001   PHE A  40 
 TRP   0.008   0.001   TRP A 278 
 HIS   0.002   0.001   HIS A 268 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.21 ( 8655)
  covalent geometry    : angle       0.50321 /  0.42 (12604)
  hydrogen bonds       : bond        0.10414 /  5.90 (  326)
  hydrogen bonds       : angle       4.61506 /  3.17 (  757)
  metal coordination   : bond        0.02238 /  1.12 (    4)
  metal coordination   : angle       3.51701 /  1.85 (    3)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8757 (mp0)
REVERT: A   76 GLU cc_start: 0.8726 (pm20) cc_final: 0.8321 (pm20)
REVERT: A  196 PHE cc_start: 0.8832 (m-80) cc_final: 0.8397 (m-80)
REVERT: A  213 ARG cc_start: 0.9017 (mtp85) cc_final: 0.8571 (mtp85)
REVERT: A  224 GLU cc_start: 0.9152 (tp30) cc_final: 0.8837 (tm-30)
REVERT: A  228 MET cc_start: 0.9252 (tpt) cc_final: 0.8932 (tmm)
REVERT: A  231 ASP cc_start: 0.8927 (t0) cc_final: 0.8581 (t0)
REVERT: A  243 HIS cc_start: 0.8330 (m-70) cc_final: 0.7783 (m90)
REVERT: A  256 GLU cc_start: 0.9256 (mp0) cc_final: 0.8927 (mp0)
REVERT: A  278 TRP cc_start: 0.8798 (m100) cc_final: 0.8496 (m100)
REVERT: A  328 LEU cc_start: 0.9591 (mm) cc_final: 0.9376 (mt)
REVERT: A  337 LYS cc_start: 0.9464 (mttm) cc_final: 0.9077 (mtmm)
REVERT: A  356 LYS cc_start: 0.8756 (mttm) cc_final: 0.8476 (mtpm)
REVERT: A  432 GLN cc_start: 0.8554 (mt0) cc_final: 0.8270 (mm-40)
REVERT: A  465 GLN cc_start: 0.8459 (mt0) cc_final: 0.8168 (mm-40)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.7741
  time to fit residues: 62.8027
Evaluate side-chains
  56 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:   30.0000
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 130 GLN
A 175 ASN
A 207 GLN
** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.074698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.046730 restraints weight = 20130.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.2581 rms_B_bonded: 2.40
r_work: 0.2428 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8860
moved from start:          0.1177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.098   8659  Z= 0.381
  Angle     :  0.612   6.393  12607  Z= 0.348
  Chirality :  0.041   0.210   1528
  Planarity :  0.006   0.073    897
  Dihedral  : 22.751 179.263   3456
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 10.49 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.40), residues: 493
  helix:  1.56 (0.41), residues: 169
  sheet: -0.61 (0.65), residues: 78
  loop : -0.02 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 461 
 TYR   0.017   0.002   TYR A   5 
 PHE   0.031   0.003   PHE A 236 
 TRP   0.010   0.002   TRP A 278 
 HIS   0.006   0.001   HIS A 428 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00746 /  0.38 ( 8655)
  covalent geometry    : angle       0.60852 /  0.35 (12604)
  hydrogen bonds       : bond        0.05998 /  3.99 (  326)
  hydrogen bonds       : angle       3.99326 /  2.79 (  757)
  metal coordination   : bond        0.00833 /  0.41 (    4)
  metal coordination   : angle       4.03126 /  2.08 (    3)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.206 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8789 (mt-10)
REVERT: A  196 PHE cc_start: 0.8961 (m-80) cc_final: 0.8746 (m-80)
REVERT: A  213 ARG cc_start: 0.8993 (mtp85) cc_final: 0.8557 (mtp85)
REVERT: A  219 LYS cc_start: 0.8827 (ttpt) cc_final: 0.8396 (tttm)
REVERT: A  224 GLU cc_start: 0.9291 (tp30) cc_final: 0.8927 (tm-30)
REVERT: A  228 MET cc_start: 0.9328 (tpt) cc_final: 0.8974 (tmm)
REVERT: A  231 ASP cc_start: 0.9031 (t0) cc_final: 0.8608 (t0)
REVERT: A  243 HIS cc_start: 0.8321 (m-70) cc_final: 0.7816 (m90)
REVERT: A  256 GLU cc_start: 0.9218 (mp0) cc_final: 0.8957 (mp0)
REVERT: A  278 TRP cc_start: 0.8890 (m100) cc_final: 0.8581 (m100)
REVERT: A  281 ARG cc_start: 0.8440 (ttm110) cc_final: 0.8034 (ttm110)
REVERT: A  328 LEU cc_start: 0.9635 (mm) cc_final: 0.9366 (mt)
REVERT: A  331 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8931 (mt-10)
REVERT: A  337 LYS cc_start: 0.9462 (mttm) cc_final: 0.8947 (mtmm)
REVERT: A  356 LYS cc_start: 0.8796 (mttm) cc_final: 0.8525 (mtpm)
REVERT: A  366 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8206 (mmm)
REVERT: A  432 GLN cc_start: 0.8630 (mt0) cc_final: 0.8358 (mm110)
REVERT: A  480 ARG cc_start: 0.8868 (ttm-80) cc_final: 0.8550 (mpp80)
  outliers start: 7
  outliers final: 2
  residues processed: 57
  average time/residue: 0.7861
  time to fit residues: 46.6754
Evaluate side-chains
  53 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 50
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  366 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 59 optimal weight:    7.9990
   chunk 7 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 60 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 28 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  82 GLN
** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 268 HIS ** 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 = 0.3270 r_free = 0.3270 target = 0.076242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.048489 restraints weight = 19865.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.2624 rms_B_bonded: 2.09
r_work: 0.2471 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8825
moved from start:          0.1066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8659  Z= 0.183
  Angle     :  0.501   6.535  12607  Z= 0.291
  Chirality :  0.035   0.193   1528
  Planarity :  0.004   0.062    897
  Dihedral  : 22.889 179.375   3456
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 13.05 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.68 (0.40), residues: 493
  helix:  1.76 (0.41), residues: 169
  sheet: -0.62 (0.64), residues: 78
  loop : -0.02 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  33 
 TYR   0.016   0.001   TYR A 340 
 PHE   0.018   0.002   PHE A  40 
 TRP   0.008   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A 268 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.18 ( 8655)
  covalent geometry    : angle       0.49776 /  0.29 (12604)
  hydrogen bonds       : bond        0.04901 /  3.27 (  326)
  hydrogen bonds       : angle       3.75884 /  2.59 (  757)
  metal coordination   : bond        0.02316 /  1.16 (    4)
  metal coordination   : angle       3.58428 /  1.88 (    3)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8783 (mmm) cc_final: 0.8532 (mmm)
REVERT: A   73 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8686 (mt-10)
REVERT: A   76 GLU cc_start: 0.8754 (pm20) cc_final: 0.8473 (pm20)
REVERT: A   84 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8949 (mm-30)
REVERT: A  219 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8402 (ptmt)
REVERT: A  224 GLU cc_start: 0.9278 (tp30) cc_final: 0.8916 (tm-30)
REVERT: A  228 MET cc_start: 0.9320 (tpt) cc_final: 0.9053 (tpt)
REVERT: A  231 ASP cc_start: 0.9021 (t0) cc_final: 0.8605 (t0)
REVERT: A  256 GLU cc_start: 0.9218 (mp0) cc_final: 0.8945 (mp0)
REVERT: A  278 TRP cc_start: 0.8837 (m100) cc_final: 0.8625 (m100)
REVERT: A  328 LEU cc_start: 0.9621 (mm) cc_final: 0.9397 (mt)
REVERT: A  337 LYS cc_start: 0.9457 (mttm) cc_final: 0.9074 (mtmm)
REVERT: A  348 CYS cc_start: 0.9188 (m) cc_final: 0.8962 (m)
REVERT: A  356 LYS cc_start: 0.8760 (mttm) cc_final: 0.8536 (mtpm)
REVERT: A  432 GLN cc_start: 0.8602 (mt0) cc_final: 0.8337 (mm-40)
REVERT: A  480 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8564 (mpp80)
  outliers start: 5
  outliers final: 2
  residues processed: 56
  average time/residue: 0.8074
  time to fit residues: 47.1093
Evaluate side-chains
  57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  480 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 13 optimal weight:    0.0770
   chunk 30 optimal weight:    0.6980
   chunk 42 optimal weight:    7.9990
   chunk 66 optimal weight:   20.0000
   chunk 47 optimal weight:    0.8980
   chunk 53 optimal weight:   10.0000
   chunk 43 optimal weight:    0.5980
   chunk 8 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 46 optimal weight:    0.2980
   overall best weight:    0.4938

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 175 ASN
** A 268 HIS ** 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 = 0.3310 r_free = 0.3310 target = 0.078308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.050624 restraints weight = 20172.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.2678 rms_B_bonded: 2.15
r_work: 0.2526 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8841
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051   8659  Z= 0.117
  Angle     :  0.478   7.911  12607  Z= 0.276
  Chirality :  0.032   0.179   1528
  Planarity :  0.004   0.053    897
  Dihedral  : 22.905 179.803   3456
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 13.52 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.40), residues: 493
  helix:  1.76 (0.41), residues: 171
  sheet: -0.51 (0.60), residues: 88
  loop :  0.04 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 213 
 TYR   0.008   0.001   TYR A   5 
 PHE   0.016   0.002   PHE A 196 
 TRP   0.004   0.001   TRP A 278 
 HIS   0.005   0.001   HIS A 243 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00222 /  0.12 ( 8655)
  covalent geometry    : angle       0.47285 /  0.28 (12604)
  hydrogen bonds       : bond        0.04390 /  2.99 (  326)
  hydrogen bonds       : angle       3.54023 /  2.41 (  757)
  metal coordination   : bond        0.02578 /  1.29 (    4)
  metal coordination   : angle       4.58476 /  2.41 (    3)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8787 (mmm) cc_final: 0.8508 (mmm)
REVERT: A   73 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8611 (mt-10)
REVERT: A   76 GLU cc_start: 0.8760 (pm20) cc_final: 0.8485 (pm20)
REVERT: A   84 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8968 (mm-30)
REVERT: A  195 ARG cc_start: 0.8704 (ptt90) cc_final: 0.8475 (ptt90)
REVERT: A  213 ARG cc_start: 0.9008 (mtp-110) cc_final: 0.8666 (mtp85)
REVERT: A  219 LYS cc_start: 0.8801 (ttpt) cc_final: 0.8279 (ttmm)
REVERT: A  224 GLU cc_start: 0.9290 (tp30) cc_final: 0.8940 (tm-30)
REVERT: A  228 MET cc_start: 0.9334 (tpt) cc_final: 0.9041 (tpt)
REVERT: A  231 ASP cc_start: 0.9026 (t0) cc_final: 0.8600 (t0)
REVERT: A  256 GLU cc_start: 0.9222 (mp0) cc_final: 0.8929 (mp0)
REVERT: A  266 GLU cc_start: 0.9125 (pm20) cc_final: 0.8759 (tm-30)
REVERT: A  278 TRP cc_start: 0.8897 (m100) cc_final: 0.8585 (m100)
REVERT: A  328 LEU cc_start: 0.9621 (mm) cc_final: 0.9378 (mt)
REVERT: A  337 LYS cc_start: 0.9438 (mttm) cc_final: 0.9060 (mtmm)
REVERT: A  356 LYS cc_start: 0.8751 (mttm) cc_final: 0.8537 (mtpm)
REVERT: A  407 ASP cc_start: 0.9199 (m-30) cc_final: 0.8956 (OUTLIER)
REVERT: A  432 GLN cc_start: 0.8633 (mt0) cc_final: 0.8387 (mm110)
REVERT: A  480 ARG cc_start: 0.8886 (ttm-80) cc_final: 0.8630 (mpp80)
  outliers start: 3
  outliers final: 5
  residues processed: 58
  average time/residue: 0.8930
  time to fit residues: 53.8573
Evaluate side-chains
  58 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 GLU
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  302 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 60 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 28 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 12 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   overall best weight:    3.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 175 ASN
** A 268 HIS ** 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 = 0.3255 r_free = 0.3255 target = 0.075505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.047670 restraints weight = 20359.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.2599 rms_B_bonded: 2.39
r_work: 0.2444 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8841
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072   8659  Z= 0.318
  Angle     :  0.545   6.864  12607  Z= 0.314
  Chirality :  0.038   0.202   1528
  Planarity :  0.004   0.056    897
  Dihedral  : 22.738 179.844   3456
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 14.22 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.67 (0.40), residues: 493
  helix:  1.69 (0.41), residues: 171
  sheet: -0.59 (0.64), residues: 78
  loop : -0.00 (0.42), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 324 
 TYR   0.018   0.002   TYR A 340 
 PHE   0.018   0.002   PHE A  40 
 TRP   0.006   0.001   TRP A 278 
 HIS   0.005   0.001   HIS A 428 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00616 /  0.32 ( 8655)
  covalent geometry    : angle       0.54248 /  0.31 (12604)
  hydrogen bonds       : bond        0.05156 /  3.45 (  326)
  hydrogen bonds       : angle       3.62829 /  2.51 (  757)
  metal coordination   : bond        0.01034 /  0.52 (    4)
  metal coordination   : angle       3.44393 /  1.79 (    3)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A    1 MET cc_start: 0.8813 (mmm) cc_final: 0.8523 (mmm)
REVERT: A   73 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8637 (mt-10)
REVERT: A   76 GLU cc_start: 0.8793 (pm20) cc_final: 0.8508 (pm20)
REVERT: A   84 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8948 (mm-30)
REVERT: A  213 ARG cc_start: 0.8980 (mtp-110) cc_final: 0.8630 (mtp85)
REVERT: A  219 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8370 (ptmt)
REVERT: A  224 GLU cc_start: 0.9267 (tp30) cc_final: 0.8940 (tm-30)
REVERT: A  228 MET cc_start: 0.9323 (tpt) cc_final: 0.9032 (tpt)
REVERT: A  231 ASP cc_start: 0.9040 (t0) cc_final: 0.8632 (t0)
REVERT: A  256 GLU cc_start: 0.9215 (mp0) cc_final: 0.8922 (mp0)
REVERT: A  259 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8697 (pt0)
REVERT: A  278 TRP cc_start: 0.8859 (m100) cc_final: 0.8529 (m100)
REVERT: A  328 LEU cc_start: 0.9630 (mm) cc_final: 0.9354 (mt)
REVERT: A  331 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8931 (mt-10)
REVERT: A  337 LYS cc_start: 0.9449 (mttm) cc_final: 0.8936 (mtmm)
REVERT: A  356 LYS cc_start: 0.8769 (mttm) cc_final: 0.8559 (mttm)
REVERT: A  432 GLN cc_start: 0.8644 (mt0) cc_final: 0.8369 (mm-40)
REVERT: A  480 ARG cc_start: 0.8884 (ttm-80) cc_final: 0.8533 (mpp80)
  outliers start: 5
  outliers final: 3
  residues processed: 57
  average time/residue: 0.9139
  time to fit residues: 54.1001
Evaluate side-chains
  56 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  302 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 5 optimal weight:    0.3980
   chunk 25 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 66 optimal weight:   20.0000
   chunk 40 optimal weight:    0.4980
   chunk 24 optimal weight:    9.9990
   chunk 9 optimal weight:    0.5980
   chunk 12 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.077744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.050042 restraints weight = 19999.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.2666 rms_B_bonded: 2.14
r_work: 0.2513 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8854
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   8659  Z= 0.124
  Angle     :  0.478   7.245  12607  Z= 0.278
  Chirality :  0.033   0.182   1528
  Planarity :  0.004   0.054    897
  Dihedral  : 22.865 179.692   3456
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.62 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.40), residues: 493
  helix:  1.79 (0.41), residues: 171
  sheet: -0.65 (0.60), residues: 88
  loop :  0.08 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 250 
 TYR   0.011   0.001   TYR A   5 
 PHE   0.015   0.001   PHE A  40 
 TRP   0.004   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A 268 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.12 ( 8655)
  covalent geometry    : angle       0.47519 /  0.28 (12604)
  hydrogen bonds       : bond        0.04400 /  3.00 (  326)
  hydrogen bonds       : angle       3.47987 /  2.38 (  757)
  metal coordination   : bond        0.02610 /  1.30 (    4)
  metal coordination   : angle       3.52828 /  1.86 (    3)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8801 (mmm) cc_final: 0.8536 (mmm)
REVERT: A   73 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8535 (mt-10)
REVERT: A   76 GLU cc_start: 0.8778 (pm20) cc_final: 0.8548 (pm20)
REVERT: A   84 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8951 (mm-30)
REVERT: A  213 ARG cc_start: 0.9011 (mtp-110) cc_final: 0.8654 (mtp85)
REVERT: A  219 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8421 (ptmt)
REVERT: A  224 GLU cc_start: 0.9272 (tp30) cc_final: 0.8909 (tm-30)
REVERT: A  228 MET cc_start: 0.9320 (tpt) cc_final: 0.9046 (tpt)
REVERT: A  231 ASP cc_start: 0.9027 (t0) cc_final: 0.8586 (t0)
REVERT: A  256 GLU cc_start: 0.9197 (mp0) cc_final: 0.8946 (mp0)
REVERT: A  259 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8715 (pt0)
REVERT: A  266 GLU cc_start: 0.9147 (pm20) cc_final: 0.8714 (tm-30)
REVERT: A  278 TRP cc_start: 0.8864 (m100) cc_final: 0.8568 (m100)
REVERT: A  328 LEU cc_start: 0.9620 (mm) cc_final: 0.9385 (mt)
REVERT: A  337 LYS cc_start: 0.9437 (mttm) cc_final: 0.9056 (mtmm)
REVERT: A  356 LYS cc_start: 0.8732 (mttm) cc_final: 0.8512 (mtpm)
REVERT: A  432 GLN cc_start: 0.8639 (mt0) cc_final: 0.8374 (mm-40)
REVERT: A  480 ARG cc_start: 0.8884 (ttm-80) cc_final: 0.8594 (mpp80)
  outliers start: 6
  outliers final: 4
  residues processed: 57
  average time/residue: 0.8425
  time to fit residues: 50.0343
Evaluate side-chains
  57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  302 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 64 optimal weight:   10.0000
   chunk 20 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0870
   chunk 60 optimal weight:   10.0000
   chunk 58 optimal weight:    8.9990
   chunk 37 optimal weight:    4.9990
   chunk 51 optimal weight:   10.0000
   chunk 50 optimal weight:    8.9990
   overall best weight:    2.6166

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.076271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.048633 restraints weight = 20374.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.2626 rms_B_bonded: 2.32
r_work: 0.2473 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8834
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   8659  Z= 0.243
  Angle     :  0.520   7.456  12607  Z= 0.300
  Chirality :  0.035   0.193   1528
  Planarity :  0.004   0.056    897
  Dihedral  : 22.763 179.604   3456
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.85 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.40), residues: 493
  helix:  1.78 (0.41), residues: 171
  sheet: -0.58 (0.64), residues: 78
  loop : -0.01 (0.42), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 281 
 TYR   0.022   0.001   TYR A 340 
 PHE   0.017   0.002   PHE A  40 
 TRP   0.006   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A 428 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00479 /  0.24 ( 8655)
  covalent geometry    : angle       0.51755 /  0.30 (12604)
  hydrogen bonds       : bond        0.04768 /  3.21 (  326)
  hydrogen bonds       : angle       3.52832 /  2.43 (  757)
  metal coordination   : bond        0.01435 /  0.72 (    4)
  metal coordination   : angle       3.25215 /  1.70 (    3)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8809 (mmm) cc_final: 0.8540 (mmm)
REVERT: A   73 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8578 (mt-10)
REVERT: A   76 GLU cc_start: 0.8764 (pm20) cc_final: 0.8349 (pm20)
REVERT: A   84 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8985 (mm-30)
REVERT: A  213 ARG cc_start: 0.8993 (mtp-110) cc_final: 0.8698 (mtp85)
REVERT: A  219 LYS cc_start: 0.8767 (ttpt) cc_final: 0.8245 (ttmm)
REVERT: A  224 GLU cc_start: 0.9252 (tp30) cc_final: 0.8940 (tm-30)
REVERT: A  228 MET cc_start: 0.9313 (tpt) cc_final: 0.9046 (tpt)
REVERT: A  231 ASP cc_start: 0.9041 (t0) cc_final: 0.8651 (t0)
REVERT: A  253 ASN cc_start: 0.8621 (m-40) cc_final: 0.8378 (m-40)
REVERT: A  256 GLU cc_start: 0.9220 (mp0) cc_final: 0.8915 (mp0)
REVERT: A  259 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8733 (pt0)
REVERT: A  266 GLU cc_start: 0.9163 (pm20) cc_final: 0.8695 (tm-30)
REVERT: A  278 TRP cc_start: 0.8829 (m100) cc_final: 0.8514 (m100)
REVERT: A  328 LEU cc_start: 0.9620 (mm) cc_final: 0.9321 (mt)
REVERT: A  331 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8922 (mt-10)
REVERT: A  337 LYS cc_start: 0.9445 (mttm) cc_final: 0.8929 (mtmm)
REVERT: A  407 ASP cc_start: 0.9205 (m-30) cc_final: 0.8956 (t0)
REVERT: A  432 GLN cc_start: 0.8646 (mt0) cc_final: 0.8377 (mm-40)
  outliers start: 6
  outliers final: 4
  residues processed: 56
  average time/residue: 0.8689
  time to fit residues: 50.6636
Evaluate side-chains
  57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  302 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 63 optimal weight:    7.9990
   chunk 44 optimal weight:    0.6980
   chunk 42 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 4 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.077959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.050283 restraints weight = 19961.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.2668 rms_B_bonded: 2.11
r_work: 0.2518 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8802
moved from start:          0.1358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8659  Z= 0.128
  Angle     :  0.469   7.095  12607  Z= 0.273
  Chirality :  0.033   0.183   1528
  Planarity :  0.004   0.054    897
  Dihedral  : 22.835 179.426   3456
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 17.02 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.40), residues: 493
  helix:  1.74 (0.41), residues: 171
  sheet: -0.70 (0.59), residues: 88
  loop :  0.11 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 281 
 TYR   0.024   0.001   TYR A 340 
 PHE   0.014   0.001   PHE A  40 
 TRP   0.004   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A 268 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.13 ( 8655)
  covalent geometry    : angle       0.46710 /  0.27 (12604)
  hydrogen bonds       : bond        0.04311 /  2.94 (  326)
  hydrogen bonds       : angle       3.43604 /  2.34 (  757)
  metal coordination   : bond        0.02210 /  1.10 (    4)
  metal coordination   : angle       3.00093 /  1.58 (    3)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8807 (mmm) cc_final: 0.8551 (mmm)
REVERT: A   73 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8507 (mt-10)
REVERT: A   76 GLU cc_start: 0.8800 (pm20) cc_final: 0.8485 (pm20)
REVERT: A   84 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8983 (mm-30)
REVERT: A  213 ARG cc_start: 0.9008 (mtp-110) cc_final: 0.8704 (mtp85)
REVERT: A  219 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8403 (ptmt)
REVERT: A  224 GLU cc_start: 0.9253 (tp30) cc_final: 0.8914 (tm-30)
REVERT: A  228 MET cc_start: 0.9288 (tpt) cc_final: 0.9041 (tpt)
REVERT: A  231 ASP cc_start: 0.9035 (t0) cc_final: 0.8624 (t0)
REVERT: A  256 GLU cc_start: 0.9203 (mp0) cc_final: 0.8894 (mp0)
REVERT: A  266 GLU cc_start: 0.9159 (pm20) cc_final: 0.8690 (tm-30)
REVERT: A  278 TRP cc_start: 0.8836 (m100) cc_final: 0.8500 (m100)
REVERT: A  328 LEU cc_start: 0.9611 (mm) cc_final: 0.9371 (mt)
REVERT: A  337 LYS cc_start: 0.9438 (mttm) cc_final: 0.9046 (mtmm)
REVERT: A  355 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8548 (mmtt)
REVERT: A  407 ASP cc_start: 0.9217 (m-30) cc_final: 0.8948 (t0)
REVERT: A  432 GLN cc_start: 0.8614 (mt0) cc_final: 0.8356 (mm-40)
REVERT: A  480 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8562 (mpp80)
  outliers start: 5
  outliers final: 4
  residues processed: 55
  average time/residue: 0.8093
  time to fit residues: 46.2793
Evaluate side-chains
  56 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  480 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 53 optimal weight:   10.0000
   overall best weight:    1.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.077785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.050095 restraints weight = 20058.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.2657 rms_B_bonded: 2.14
r_work: 0.2503 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8857
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8659  Z= 0.166
  Angle     :  0.486   7.517  12607  Z= 0.281
  Chirality :  0.033   0.186   1528
  Planarity :  0.004   0.055    897
  Dihedral  : 22.772 179.217   3456
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 17.02 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.72 (0.40), residues: 493
  helix:  1.73 (0.41), residues: 171
  sheet: -0.69 (0.59), residues: 88
  loop :  0.13 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 281 
 TYR   0.011   0.001   TYR A   5 
 PHE   0.014   0.001   PHE A  40 
 TRP   0.006   0.001   TRP A 278 
 HIS   0.003   0.001   HIS A 268 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.17 ( 8655)
  covalent geometry    : angle       0.48442 /  0.28 (12604)
  hydrogen bonds       : bond        0.04357 /  2.96 (  326)
  hydrogen bonds       : angle       3.43782 /  2.35 (  757)
  metal coordination   : bond        0.01788 /  0.89 (    4)
  metal coordination   : angle       2.84705 /  1.49 (    3)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8600 (mt-10)
REVERT: A   76 GLU cc_start: 0.8786 (pm20) cc_final: 0.8530 (pm20)
REVERT: A   84 GLU cc_start: 0.9295 (mt-10) cc_final: 0.9006 (mm-30)
REVERT: A  213 ARG cc_start: 0.9008 (mtp-110) cc_final: 0.8700 (mtp85)
REVERT: A  219 LYS cc_start: 0.8806 (ttpt) cc_final: 0.8445 (ptmt)
REVERT: A  224 GLU cc_start: 0.9247 (tp30) cc_final: 0.8933 (tm-30)
REVERT: A  228 MET cc_start: 0.9300 (tpt) cc_final: 0.9033 (tpt)
REVERT: A  231 ASP cc_start: 0.9037 (t0) cc_final: 0.8663 (t0)
REVERT: A  256 GLU cc_start: 0.9208 (mp0) cc_final: 0.8898 (mp0)
REVERT: A  266 GLU cc_start: 0.9158 (pm20) cc_final: 0.8670 (tm-30)
REVERT: A  278 TRP cc_start: 0.8846 (m100) cc_final: 0.8510 (m100)
REVERT: A  279 GLU cc_start: 0.9449 (tt0) cc_final: 0.9232 (pt0)
REVERT: A  328 LEU cc_start: 0.9623 (mm) cc_final: 0.9383 (mt)
REVERT: A  337 LYS cc_start: 0.9441 (mttm) cc_final: 0.9031 (mtmm)
REVERT: A  407 ASP cc_start: 0.9212 (m-30) cc_final: 0.8992 (t0)
REVERT: A  432 GLN cc_start: 0.8644 (mt0) cc_final: 0.8396 (mm-40)
REVERT: A  480 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8557 (mpp80)
  outliers start: 6
  outliers final: 5
  residues processed: 55
  average time/residue: 0.8263
  time to fit residues: 47.3474
Evaluate side-chains
  55 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  480 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 59 optimal weight:   10.0000
   chunk 23 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 62 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.077394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.049712 restraints weight = 20140.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.2652 rms_B_bonded: 2.11
r_work: 0.2502 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work: 0.2385 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8860
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8659  Z= 0.193
  Angle     :  0.512   7.754  12607  Z= 0.292
  Chirality :  0.034   0.188   1528
  Planarity :  0.004   0.055    897
  Dihedral  : 22.753 179.222   3456
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 17.72 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.40), residues: 493
  helix:  1.69 (0.41), residues: 171
  sheet: -0.68 (0.59), residues: 88
  loop :  0.16 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 281 
 TYR   0.023   0.001   TYR A 340 
 PHE   0.015   0.001   PHE A  40 
 TRP   0.011   0.001   TRP A 278 
 HIS   0.003   0.001   HIS A 268 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00379 /  0.19 ( 8655)
  covalent geometry    : angle       0.51004 /  0.29 (12604)
  hydrogen bonds       : bond        0.04405 /  2.99 (  326)
  hydrogen bonds       : angle       3.44911 /  2.36 (  757)
  metal coordination   : bond        0.01610 /  0.81 (    4)
  metal coordination   : angle       2.83917 /  1.49 (    3)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8589 (mt-10)
REVERT: A   76 GLU cc_start: 0.8790 (pm20) cc_final: 0.8454 (pm20)
REVERT: A   84 GLU cc_start: 0.9404 (mt-10) cc_final: 0.9120 (mm-30)
REVERT: A  213 ARG cc_start: 0.9056 (mtp-110) cc_final: 0.8760 (mtp85)
REVERT: A  219 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8417 (ptmt)
REVERT: A  224 GLU cc_start: 0.9261 (tp30) cc_final: 0.8955 (tm-30)
REVERT: A  228 MET cc_start: 0.9296 (tpt) cc_final: 0.9019 (tpt)
REVERT: A  231 ASP cc_start: 0.9053 (t0) cc_final: 0.8677 (t0)
REVERT: A  256 GLU cc_start: 0.9251 (mp0) cc_final: 0.8949 (mp0)
REVERT: A  266 GLU cc_start: 0.9207 (pm20) cc_final: 0.8694 (tm-30)
REVERT: A  278 TRP cc_start: 0.8783 (m100) cc_final: 0.8431 (m100)
REVERT: A  279 GLU cc_start: 0.9444 (tt0) cc_final: 0.9230 (pt0)
REVERT: A  328 LEU cc_start: 0.9628 (mm) cc_final: 0.9385 (mt)
REVERT: A  337 LYS cc_start: 0.9463 (mttm) cc_final: 0.9076 (mtmm)
REVERT: A  407 ASP cc_start: 0.9308 (m-30) cc_final: 0.9005 (t0)
REVERT: A  432 GLN cc_start: 0.8695 (mt0) cc_final: 0.8407 (mm-40)
REVERT: A  480 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8604 (mpp80)
  outliers start: 7
  outliers final: 5
  residues processed: 55
  average time/residue: 0.8194
  time to fit residues: 46.8864
Evaluate side-chains
  56 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  480 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 57 optimal weight:   10.0000
   chunk 1 optimal weight:    6.9990
   chunk 52 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 49 optimal weight:    8.9990
   chunk 35 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 175 ASN
** A 268 HIS ** 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 = 0.3321 r_free = 0.3321 target = 0.078889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.051253 restraints weight = 20021.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.2691 rms_B_bonded: 2.15
r_work: 0.2539 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8841
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   8659  Z= 0.123
  Angle     :  0.496   8.915  12607  Z= 0.282
  Chirality :  0.032   0.178   1528
  Planarity :  0.004   0.053    897
  Dihedral  : 22.795 178.958   3456
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 18.41 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.40), residues: 493
  helix:  1.72 (0.41), residues: 171
  sheet: -0.67 (0.59), residues: 88
  loop :  0.09 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 281 
 TYR   0.025   0.001   TYR A 340 
 PHE   0.011   0.001   PHE A  40 
 TRP   0.005   0.001   TRP A 278 
 HIS   0.003   0.001   HIS A 268 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.12 ( 8655)
  covalent geometry    : angle       0.49439 /  0.28 (12604)
  hydrogen bonds       : bond        0.04102 /  2.82 (  326)
  hydrogen bonds       : angle       3.37816 /  2.30 (  757)
  metal coordination   : bond        0.01951 /  0.98 (    4)
  metal coordination   : angle       2.76565 /  1.46 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2252.47 seconds
wall clock time: 39 minutes 13.99 seconds (2353.99 seconds total)