Starting phenix.real_space_refine
on Tue Aug  4 15:59:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vxt_65440/08_2026/9vxt_65440.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vxt_65440/08_2026/9vxt_65440.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vxt_65440/08_2026/9vxt_65440.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vxt_65440/08_2026/9vxt_65440.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vxt_65440/08_2026/9vxt_65440.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vxt_65440/08_2026/9vxt_65440.cif"
  }
  resolution = 3.9
  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=   0.007 sd=   0.093
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    2946      2.51       5
     N     796      2.21       5
     O     814      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4580
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2290
          Classifications: {'peptide': 292}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 13, 'TRANS': 278}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 2290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2290
          Classifications: {'peptide': 292}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 13, 'TRANS': 278}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 18
  Time building chain proxies: 0.88, per 1000 atoms: 0.19
  Number of scatterers: 4580
  At special positions: 0
  Unit cell: (61.32, 86.14, 103.66, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O     814      8.00
     N     796      7.00
     C    2946      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: 0.24
  Conformation dependent library (CDL) restraints added in 93.2 milliseconds
  

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1100

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 2 sheets defined
      60.3% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 35
      removed outlier: 4.229A  pdb=" N   LYS A  20 " --> pdb=" O   HIS A  16 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   GLY A  35 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 70
    Processing helix  chain 'A' and resid 82 through 90
      removed outlier: 3.614A  pdb=" N   GLY A  90 " --> pdb=" O   ARG A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 105
    Processing helix  chain 'A' and resid 118 through 134
      removed outlier: 4.045A  pdb=" N   ALA A 122 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 150
    Processing helix  chain 'A' and resid 157 through 183
      removed outlier: 3.652A  pdb=" N   TYR A 167 " --> pdb=" O   TYR A 163 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ARG A 169 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   LEU A 170 " --> pdb=" O   GLY A 166 " (cutoff:3.500A)
      Proline residue:  A 173  - end of helix
      removed outlier: 4.033A  pdb=" N   GLN A 176 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   ALA A 177 " --> pdb=" O   PRO A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 186
      No H-bonds generated for 'chain 'A' and resid 184 through 186'
    Processing helix  chain 'A' and resid 262 through 274
      removed outlier: 3.681A  pdb=" N   GLN A 266 " --> pdb=" O   ALA A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 302
    Processing helix  chain 'A' and resid 324 through 336
      removed outlier: 3.762A  pdb=" N   GLU A 328 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 35
      removed outlier: 3.908A  pdb=" N   LYS B  20 " --> pdb=" O   HIS B  16 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   GLY B  35 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 70
      removed outlier: 3.624A  pdb=" N   GLU B  68 " --> pdb=" O   CYS B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 90
    Processing helix  chain 'B' and resid 91 through 105
    Processing helix  chain 'B' and resid 119 through 134
      removed outlier: 3.614A  pdb=" N   LEU B 123 " --> pdb=" O   TRP B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 150
    Processing helix  chain 'B' and resid 156 through 184
      removed outlier: 3.609A  pdb=" N   TYR B 167 " --> pdb=" O   TYR B 163 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   ARG B 169 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 5.222A  pdb=" N   LEU B 170 " --> pdb=" O   GLY B 166 " (cutoff:3.500A)
      Proline residue:  B 173  - end of helix
      removed outlier: 3.997A  pdb=" N   GLN B 176 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   ALA B 177 " --> pdb=" O   PRO B 173 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLN B 184 " --> pdb=" O   ARG B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 274
      removed outlier: 4.055A  pdb=" N   GLN B 266 " --> pdb=" O   ALA B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 302
    Processing helix  chain 'B' and resid 324 through 336
      removed outlier: 3.869A  pdb=" N   GLU B 328 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 224
      removed outlier: 7.403A  pdb=" N   ILE A 244 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   SER A 243 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   TYR A 199 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLU A 260 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   LEU A 198 " --> pdb=" O   ARG A 310 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   ILE A 312 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   ILE A 200 " --> pdb=" O   ILE A 312 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   TYR A 314 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   LEU A 202 " --> pdb=" O   TYR A 314 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 220 through 223
      removed outlier: 6.154A  pdb=" N   PHE B 221 " --> pdb=" O   GLU B 246 " (cutoff:3.500A)
      removed outlier: 5.928A  pdb=" N   GLU B 246 " --> pdb=" O   PHE B 221 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ASP B 223 " --> pdb=" O   ILE B 244 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   TYR B 199 " --> pdb=" O   VAL B 258 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLU B 260 " --> pdb=" O   TYR B 199 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   LEU B 198 " --> pdb=" O   ARG B 310 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   ILE B 312 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   ILE B 200 " --> pdb=" O   ILE B 312 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   TYR B 314 " --> pdb=" O   ILE B 200 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   LEU B 202 " --> pdb=" O   TYR B 314 " (cutoff:3.500A)

    255 hydrogen bonds defined for protein.
    753 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.38

  Time building geometry restraints manager: 0.32 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: 1485
        1.34 -     1.46: 1070
        1.46 -     1.58: 2087
        1.58 -     1.70: 0
        1.70 -     1.81: 28
  Bond restraints: 4670
  Sorted by residual:
  bond pdb=" CG  LEU B 330 "
       pdb=" CD2 LEU B 330 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.63e+00
  bond pdb=" CB  ARG A 178 "
       pdb=" CG  ARG A 178 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.88e-01
  bond pdb=" CA  ASN B 211 "
       pdb=" CB  ASN B 211 "
    ideal  model  delta    sigma   weight residual
    1.536  1.553 -0.018 2.08e-02 2.31e+03 7.19e-01
  bond pdb=" CA  ILE B  73 "
       pdb=" CB  ILE B  73 "
    ideal  model  delta    sigma   weight residual
    1.545  1.538  0.007 9.10e-03 1.21e+04 6.60e-01
  bond pdb=" CB  ASN B 211 "
       pdb=" CG  ASN B 211 "
    ideal  model  delta    sigma   weight residual
    1.516  1.535 -0.019 2.50e-02 1.60e+03 5.56e-01
  ... (remaining 4665 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.81: 6285
        2.81 -     5.63: 39
        5.63 -     8.44: 9
        8.44 -    11.25: 1
       11.25 -    14.07: 2
  Bond angle restraints: 6336
  Sorted by residual:
  angle pdb=" CA  LEU B 330 "
        pdb=" CB  LEU B 330 "
        pdb=" CG  LEU B 330 "
      ideal   model   delta    sigma   weight residual
     116.30  130.37  -14.07 3.50e+00 8.16e-02 1.62e+01
  angle pdb=" C   VAL B 329 "
        pdb=" N   LEU B 330 "
        pdb=" CA  LEU B 330 "
      ideal   model   delta    sigma   weight residual
     120.31  114.54    5.77 1.52e+00 4.33e-01 1.44e+01
  angle pdb=" CA  LEU A 202 "
        pdb=" CB  LEU A 202 "
        pdb=" CG  LEU A 202 "
      ideal   model   delta    sigma   weight residual
     116.30  128.65  -12.35 3.50e+00 8.16e-02 1.24e+01
  angle pdb=" N   LEU B 330 "
        pdb=" CA  LEU B 330 "
        pdb=" CB  LEU B 330 "
      ideal   model   delta    sigma   weight residual
     110.28  114.98   -4.70 1.55e+00 4.16e-01 9.19e+00
  angle pdb=" CA  LEU A  26 "
        pdb=" CB  LEU A  26 "
        pdb=" CG  LEU A  26 "
      ideal   model   delta    sigma   weight residual
     116.30  125.89   -9.59 3.50e+00 8.16e-02 7.52e+00
  ... (remaining 6331 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.13: 2455
       14.13 -    28.26: 225
       28.26 -    42.39: 87
       42.39 -    56.51: 8
       56.51 -    70.64: 5
  Dihedral angle restraints: 2780
    sinusoidal: 1080
      harmonic: 1700
  Sorted by residual:
  dihedral pdb=" CG  ARG B 334 "
           pdb=" CD  ARG B 334 "
           pdb=" NE  ARG B 334 "
           pdb=" CZ  ARG B 334 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.41   44.41     2      1.50e+01 4.44e-03 1.04e+01
  dihedral pdb=" CA  LEU A 225 "
           pdb=" C   LEU A 225 "
           pdb=" N   PRO A 226 "
           pdb=" CA  PRO A 226 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.10  -15.90     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CG  ARG B 281 "
           pdb=" CD  ARG B 281 "
           pdb=" NE  ARG B 281 "
           pdb=" CZ  ARG B 281 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -131.93   41.93     2      1.50e+01 4.44e-03 9.53e+00
  ... (remaining 2777 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 502
       0.035 -    0.070: 169
       0.070 -    0.105: 42
       0.105 -    0.140: 16
       0.140 -    0.175: 1
  Chirality restraints: 730
  Sorted by residual:
  chirality pdb=" CG  LEU A  26 "
            pdb=" CB  LEU A  26 "
            pdb=" CD1 LEU A  26 "
            pdb=" CD2 LEU A  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.64e-01
  chirality pdb=" CA  ILE A  10 "
            pdb=" N   ILE A  10 "
            pdb=" C   ILE A  10 "
            pdb=" CB  ILE A  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.65e-01
  chirality pdb=" CA  GLN A  55 "
            pdb=" N   GLN A  55 "
            pdb=" C   GLN A  55 "
            pdb=" CB  GLN A  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.43e-01
  ... (remaining 727 not shown)

  Planarity restraints: 798
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 202 "   -0.024 5.00e-02 4.00e+02   3.64e-02 2.12e+00
        pdb=" N   PRO A 203 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 203 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 203 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 302 "    0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO A 303 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 303 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 303 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 140 "   -0.023 5.00e-02 4.00e+02   3.43e-02 1.89e+00
        pdb=" N   PRO A 141 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 141 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 141 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 795 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 54
        2.68 -     3.24: 4447
        3.24 -     3.79: 6961
        3.79 -     4.35: 8499
        4.35 -     4.90: 13718
  Nonbonded interactions: 33679
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 178 "
            pdb=" O   PRO A 226 "
     model   vdw
     2.126 3.120
  nonbonded pdb=" O   LEU A  51 "
            pdb=" NE2 GLN A  55 "
     model   vdw
     2.195 3.120
  nonbonded pdb=" O   LEU B  51 "
            pdb=" NE2 GLN B  55 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" NH2 ARG A  76 "
            pdb=" OG  SER B 145 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" O   HIS A  50 "
            pdb=" OG  SER A  53 "
     model   vdw
     2.347 3.040
  ... (remaining 33674 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.160
  Set stop_for_unknowns flag:              0.010
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.030
  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:0.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5960
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   0.042   4670  Z= 0.119
  Angle     :  0.671  14.067   6336  Z= 0.319
  Chirality :  0.040   0.175    730
  Planarity :  0.004   0.036    798
  Dihedral  : 12.671  70.643   1680
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.54 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.38), residues: 552
  helix:  1.92 (0.29), residues: 322
  sheet: -1.04 (0.80), residues: 46
  loop : -1.05 (0.48), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  95 
 TYR   0.013   0.001   TYR A 182 
 PHE   0.006   0.001   PHE A 153 
 TRP   0.022   0.002   TRP A  34 
 HIS   0.006   0.001   HIS B  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.12 ( 4670)
  covalent geometry    : angle       0.67123 /  0.32 ( 6336)
  hydrogen bonds       : bond        0.11412 /  8.19 (  255)
  hydrogen bonds       : angle       4.65320 /  3.40 (  753)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 HIS cc_start: 0.7392 (p90) cc_final: 0.7049 (p-80)
REVERT: A  178 ARG cc_start: 0.5930 (ttt-90) cc_final: 0.5511 (ttt-90)
REVERT: A  196 GLN cc_start: 0.8585 (tt0) cc_final: 0.7796 (tm-30)
REVERT: A  199 TYR cc_start: 0.7580 (m-80) cc_final: 0.6822 (m-80)
REVERT: A  223 ASP cc_start: 0.7473 (t70) cc_final: 0.7097 (t70)
REVERT: A  261 TYR cc_start: 0.6906 (m-80) cc_final: 0.6542 (m-10)
REVERT: A  297 ASP cc_start: 0.7805 (t0) cc_final: 0.7521 (t0)
REVERT: B   77 TYR cc_start: 0.7986 (m-80) cc_final: 0.7576 (m-10)
REVERT: B  196 GLN cc_start: 0.8633 (tt0) cc_final: 0.7891 (tm-30)
REVERT: B  199 TYR cc_start: 0.7685 (m-80) cc_final: 0.6864 (m-80)
REVERT: B  271 MET cc_start: 0.7746 (mtm) cc_final: 0.7116 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0482
  time to fit residues: 6.8397
Evaluate side-chains
  77 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    8.9990
   chunk 48 optimal weight:    9.9990
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    0.4980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:   20.0000
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.1980
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  55 GLN
A  61 ASN
B  55 GLN
B  61 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.238045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.210878 restraints weight = 6008.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.216630 restraints weight = 3603.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.220648 restraints weight = 2398.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.223414 restraints weight = 1714.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.225573 restraints weight = 1299.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.4416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6092
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4670  Z= 0.109
  Angle     :  0.591  13.586   6336  Z= 0.272
  Chirality :  0.041   0.413    730
  Planarity :  0.004   0.031    798
  Dihedral  :  3.536  15.272    638
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.72 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.26 %
    Favored  : 88.68 %
  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:  1.20 (0.37), residues: 552
  helix:  1.99 (0.29), residues: 324
  sheet: -0.77 (0.71), residues: 58
  loop : -0.97 (0.50), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  76 
 TYR   0.017   0.001   TYR A 182 
 PHE   0.013   0.001   PHE B 323 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.11 ( 4670)
  covalent geometry    : angle       0.59066 /  0.27 ( 6336)
  hydrogen bonds       : bond        0.03258 /  2.31 (  255)
  hydrogen bonds       : angle       4.14270 /  3.01 (  753)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 ARG cc_start: 0.5849 (ttt-90) cc_final: 0.5061 (ttt-90)
REVERT: A  195 SER cc_start: 0.9117 (t) cc_final: 0.8010 (p)
REVERT: A  196 GLN cc_start: 0.8691 (tt0) cc_final: 0.7772 (tm-30)
REVERT: A  199 TYR cc_start: 0.7512 (m-80) cc_final: 0.6927 (m-80)
REVERT: A  223 ASP cc_start: 0.7446 (t70) cc_final: 0.7126 (t70)
REVERT: A  261 TYR cc_start: 0.6831 (m-80) cc_final: 0.6409 (m-10)
REVERT: B  196 GLN cc_start: 0.8737 (tt0) cc_final: 0.8013 (tm-30)
REVERT: B  199 TYR cc_start: 0.7695 (m-80) cc_final: 0.7100 (m-80)
REVERT: B  257 CYS cc_start: 0.7837 (t) cc_final: 0.6902 (t)
  outliers start: 10
  outliers final: 8
  residues processed: 90
  average time/residue: 0.0495
  time to fit residues: 5.7866
Evaluate side-chains
  86 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain B residue   34 TRP
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  148 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 4 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0570
   overall best weight:    0.9500

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  16 HIS
A 308 ASN
B  61 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.235304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.208188 restraints weight = 6059.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.213901 restraints weight = 3605.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.217962 restraints weight = 2383.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.220598 restraints weight = 1695.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.222849 restraints weight = 1291.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.4393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6152
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4670  Z= 0.117
  Angle     :  0.574   8.294   6336  Z= 0.270
  Chirality :  0.039   0.320    730
  Planarity :  0.004   0.032    798
  Dihedral  :  3.521  12.128    638
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.90 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 10.29 %
    Favored  : 86.63 %
  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:  1.39 (0.37), residues: 552
  helix:  2.15 (0.29), residues: 324
  sheet: -0.69 (0.71), residues: 58
  loop : -0.91 (0.50), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 178 
 TYR   0.014   0.001   TYR A 104 
 PHE   0.014   0.002   PHE A 323 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 ( 4670)
  covalent geometry    : angle       0.57426 /  0.27 ( 6336)
  hydrogen bonds       : bond        0.03190 /  2.27 (  255)
  hydrogen bonds       : angle       4.08578 /  2.96 (  753)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.103 
Fit side-chains
REVERT: A   16 HIS cc_start: 0.7123 (p90) cc_final: 0.6879 (p90)
REVERT: A  178 ARG cc_start: 0.6159 (ttt-90) cc_final: 0.5351 (ttt-90)
REVERT: A  196 GLN cc_start: 0.8755 (tt0) cc_final: 0.7900 (tm-30)
REVERT: A  199 TYR cc_start: 0.7527 (m-80) cc_final: 0.7026 (m-80)
REVERT: A  261 TYR cc_start: 0.6785 (m-80) cc_final: 0.6396 (m-10)
REVERT: B  196 GLN cc_start: 0.8716 (tt0) cc_final: 0.7953 (tm-30)
REVERT: B  199 TYR cc_start: 0.7766 (m-80) cc_final: 0.7021 (m-80)
REVERT: B  257 CYS cc_start: 0.7849 (t) cc_final: 0.6758 (t)
  outliers start: 15
  outliers final: 11
  residues processed: 91
  average time/residue: 0.0460
  time to fit residues: 5.5825
Evaluate side-chains
  91 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 TRP
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain B residue   34 TRP
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  208 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0770
   chunk 46 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0050
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.8156

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  61 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.234554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.207033 restraints weight = 6019.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.212878 restraints weight = 3595.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.216919 restraints weight = 2380.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.219901 restraints weight = 1699.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.222069 restraints weight = 1280.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.4390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6196
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4670  Z= 0.107
  Angle     :  0.577   8.415   6336  Z= 0.265
  Chirality :  0.039   0.306    730
  Planarity :  0.004   0.033    798
  Dihedral  :  3.453  12.282    638
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.90 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 13.79 %
    Favored  : 83.33 %
  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:  1.52 (0.37), residues: 552
  helix:  2.20 (0.28), residues: 326
  sheet: -1.00 (0.66), residues: 64
  loop : -0.58 (0.53), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 180 
 TYR   0.012   0.001   TYR A 104 
 PHE   0.008   0.001   PHE A 279 
 TRP   0.013   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.11 ( 4670)
  covalent geometry    : angle       0.57729 /  0.27 ( 6336)
  hydrogen bonds       : bond        0.03071 /  2.17 (  255)
  hydrogen bonds       : angle       3.98979 /  2.89 (  753)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A   16 HIS cc_start: 0.7052 (p90) cc_final: 0.6650 (p90)
REVERT: A  178 ARG cc_start: 0.5986 (ttt-90) cc_final: 0.5287 (ttt-90)
REVERT: A  196 GLN cc_start: 0.8720 (tt0) cc_final: 0.7904 (tm-30)
REVERT: A  199 TYR cc_start: 0.7500 (m-80) cc_final: 0.7058 (m-80)
REVERT: B  180 ARG cc_start: 0.6277 (ttp-110) cc_final: 0.5521 (tpt90)
REVERT: B  196 GLN cc_start: 0.8721 (tt0) cc_final: 0.8002 (tm-30)
REVERT: B  199 TYR cc_start: 0.7711 (m-80) cc_final: 0.7068 (m-80)
REVERT: B  257 CYS cc_start: 0.7901 (t) cc_final: 0.7017 (t)
  outliers start: 14
  outliers final: 12
  residues processed: 91
  average time/residue: 0.0498
  time to fit residues: 6.0743
Evaluate side-chains
  94 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 TRP
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain B residue   34 TRP
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  208 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 18 optimal weight:    0.6980
   chunk 1 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 39 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    2.2786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  55 GLN
** B 196 GLN ** 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 = 0.4601 r_free = 0.4601 target = 0.246064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.224575 restraints weight = 5785.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.229187 restraints weight = 3564.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.232512 restraints weight = 2404.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.234546 restraints weight = 1736.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.236356 restraints weight = 1342.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.4506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6500
moved from start:          0.3623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   4670  Z= 0.198
  Angle     :  0.753  11.791   6336  Z= 0.352
  Chirality :  0.044   0.310    730
  Planarity :  0.005   0.035    798
  Dihedral  :  4.120  12.001    638
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.80 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 14.81 %
    Favored  : 81.28 %
  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:  0.83 (0.37), residues: 552
  helix:  1.60 (0.28), residues: 324
  sheet: -1.41 (0.63), residues: 64
  loop : -0.63 (0.54), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 197 
 TYR   0.026   0.003   TYR A 104 
 PHE   0.015   0.003   PHE A 117 
 TRP   0.023   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00452 /  0.20 ( 4670)
  covalent geometry    : angle       0.75268 /  0.35 ( 6336)
  hydrogen bonds       : bond        0.04307 /  2.97 (  255)
  hydrogen bonds       : angle       4.59765 /  3.37 (  753)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 HIS cc_start: 0.7262 (p90) cc_final: 0.6962 (p90)
REVERT: A  106 TYR cc_start: 0.5995 (OUTLIER) cc_final: 0.5302 (t80)
REVERT: A  196 GLN cc_start: 0.8539 (tt0) cc_final: 0.8003 (tm-30)
REVERT: B   10 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7318 (pt)
REVERT: B  106 TYR cc_start: 0.6490 (OUTLIER) cc_final: 0.5664 (t80)
REVERT: B  196 GLN cc_start: 0.8391 (tt0) cc_final: 0.7605 (tm-30)
REVERT: B  197 ARG cc_start: 0.6550 (mmt90) cc_final: 0.6327 (mmt90)
REVERT: B  199 TYR cc_start: 0.7687 (m-80) cc_final: 0.7356 (m-80)
REVERT: B  257 CYS cc_start: 0.8104 (t) cc_final: 0.7558 (t)
  outliers start: 19
  outliers final: 14
  residues processed: 97
  average time/residue: 0.0440
  time to fit residues: 5.8011
Evaluate side-chains
  97 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue  106 TYR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain B residue   10 ILE
Chi-restraints excluded: chain B residue   34 TRP
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  208 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 45 optimal weight:    0.0970
   chunk 39 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 42 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.9380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  55 GLN
B  61 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.227633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.200968 restraints weight = 6461.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.206517 restraints weight = 3846.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.210480 restraints weight = 2558.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.213300 restraints weight = 1833.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.215387 restraints weight = 1383.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6330
moved from start:          0.3655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4670  Z= 0.120
  Angle     :  0.629  10.169   6336  Z= 0.286
  Chirality :  0.040   0.256    730
  Planarity :  0.004   0.034    798
  Dihedral  :  3.676  12.576    638
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.08 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 16.87 %
    Favored  : 79.42 %
  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:  1.17 (0.38), residues: 552
  helix:  1.94 (0.28), residues: 324
  sheet: -1.40 (0.65), residues: 64
  loop : -0.60 (0.54), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 180 
 TYR   0.014   0.002   TYR B 182 
 PHE   0.009   0.001   PHE A 117 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 ( 4670)
  covalent geometry    : angle       0.62900 /  0.29 ( 6336)
  hydrogen bonds       : bond        0.03266 /  2.28 (  255)
  hydrogen bonds       : angle       4.10498 /  2.99 (  753)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 TRP cc_start: 0.5906 (OUTLIER) cc_final: 0.4482 (t60)
REVERT: A  196 GLN cc_start: 0.8715 (tt0) cc_final: 0.7947 (tm-30)
REVERT: B  196 GLN cc_start: 0.8687 (tt0) cc_final: 0.8016 (tm-30)
REVERT: B  197 ARG cc_start: 0.6461 (mmt90) cc_final: 0.6120 (mmt90)
REVERT: B  199 TYR cc_start: 0.7741 (m-80) cc_final: 0.7186 (m-80)
REVERT: B  257 CYS cc_start: 0.7889 (t) cc_final: 0.7177 (t)
  outliers start: 18
  outliers final: 11
  residues processed: 94
  average time/residue: 0.0505
  time to fit residues: 6.3305
Evaluate side-chains
  92 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue  119 TRP
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain B residue   34 TRP
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  208 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  55 GLN
B 183 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.247486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.226712 restraints weight = 5860.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.231276 restraints weight = 3589.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.234322 restraints weight = 2423.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.236789 restraints weight = 1763.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.238240 restraints weight = 1337.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.4520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6441
moved from start:          0.3999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4670  Z= 0.139
  Angle     :  0.663   9.631   6336  Z= 0.306
  Chirality :  0.041   0.264    730
  Planarity :  0.004   0.034    798
  Dihedral  :  3.704  12.921    638
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.44 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 17.70 %
    Favored  : 78.40 %
  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:  1.10 (0.37), residues: 552
  helix:  1.91 (0.28), residues: 324
  sheet: -1.44 (0.64), residues: 64
  loop : -0.68 (0.54), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 180 
 TYR   0.025   0.002   TYR B 314 
 PHE   0.010   0.001   PHE A 117 
 TRP   0.008   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 ( 4670)
  covalent geometry    : angle       0.66344 /  0.31 ( 6336)
  hydrogen bonds       : bond        0.03533 /  2.46 (  255)
  hydrogen bonds       : angle       4.15452 /  3.03 (  753)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 HIS cc_start: 0.7061 (p90) cc_final: 0.6848 (p90)
REVERT: A  106 TYR cc_start: 0.6445 (OUTLIER) cc_final: 0.5427 (t80)
REVERT: A  119 TRP cc_start: 0.6212 (OUTLIER) cc_final: 0.4709 (t60)
REVERT: A  120 MET cc_start: 0.6560 (ppp) cc_final: 0.6258 (ppp)
REVERT: A  196 GLN cc_start: 0.8409 (tt0) cc_final: 0.7848 (tm-30)
REVERT: A  199 TYR cc_start: 0.7729 (m-80) cc_final: 0.7075 (m-80)
REVERT: B  196 GLN cc_start: 0.8397 (tt0) cc_final: 0.7792 (tm-30)
REVERT: B  199 TYR cc_start: 0.7737 (m-80) cc_final: 0.7402 (m-80)
REVERT: B  257 CYS cc_start: 0.8106 (t) cc_final: 0.7523 (t)
  outliers start: 19
  outliers final: 16
  residues processed: 93
  average time/residue: 0.0411
  time to fit residues: 5.1471
Evaluate side-chains
  98 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ILE
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue  106 TYR
Chi-restraints excluded: chain A residue  119 TRP
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain B residue   34 TRP
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  208 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 8 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  55 GLN
B 176 GLN
B 184 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.227486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.200998 restraints weight = 6547.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.206459 restraints weight = 3878.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.210376 restraints weight = 2578.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.213233 restraints weight = 1851.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.215240 restraints weight = 1405.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.4312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6330
moved from start:          0.4150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4670  Z= 0.121
  Angle     :  0.636   9.139   6336  Z= 0.293
  Chirality :  0.040   0.299    730
  Planarity :  0.004   0.036    798
  Dihedral  :  3.553  12.053    638
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.08 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 19.34 %
    Favored  : 77.37 %
  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:  1.14 (0.37), residues: 552
  helix:  1.98 (0.28), residues: 324
  sheet: -1.47 (0.63), residues: 68
  loop : -0.70 (0.54), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 180 
 TYR   0.018   0.001   TYR B 182 
 PHE   0.009   0.001   PHE A 279 
 TRP   0.005   0.001   TRP A 119 
 HIS   0.003   0.001   HIS B  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.12 ( 4670)
  covalent geometry    : angle       0.63593 /  0.29 ( 6336)
  hydrogen bonds       : bond        0.03242 /  2.25 (  255)
  hydrogen bonds       : angle       3.98651 /  2.90 (  753)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 TRP cc_start: 0.6092 (OUTLIER) cc_final: 0.5293 (m-10)
REVERT: A  168 LEU cc_start: 0.8458 (mp) cc_final: 0.8170 (mp)
REVERT: A  196 GLN cc_start: 0.8663 (tt0) cc_final: 0.7878 (tm-30)
REVERT: A  199 TYR cc_start: 0.7796 (m-80) cc_final: 0.6958 (m-80)
REVERT: B  106 TYR cc_start: 0.6048 (OUTLIER) cc_final: 0.5369 (t80)
REVERT: B  196 GLN cc_start: 0.8681 (tt0) cc_final: 0.7717 (tm-30)
REVERT: B  199 TYR cc_start: 0.7797 (m-80) cc_final: 0.7197 (m-80)
REVERT: B  257 CYS cc_start: 0.7918 (t) cc_final: 0.7155 (t)
  outliers start: 16
  outliers final: 13
  residues processed: 92
  average time/residue: 0.0444
  time to fit residues: 5.6060
Evaluate side-chains
  94 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue  119 TRP
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain B residue   10 ILE
Chi-restraints excluded: chain B residue   34 TRP
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  208 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 23 optimal weight:    0.2980
   chunk 6 optimal weight:    0.0000
   chunk 39 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0570
   overall best weight:    0.3702

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  55 GLN
B  55 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.232569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.206552 restraints weight = 6218.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.212128 restraints weight = 3674.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.216112 restraints weight = 2414.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.218936 restraints weight = 1719.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.221060 restraints weight = 1304.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.4362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6244
moved from start:          0.4227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4670  Z= 0.107
  Angle     :  0.618   9.539   6336  Z= 0.285
  Chirality :  0.038   0.205    730
  Planarity :  0.004   0.035    798
  Dihedral  :  3.484  18.700    638
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 20.16 %
    Favored  : 77.78 %
  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:  1.23 (0.37), residues: 552
  helix:  2.06 (0.28), residues: 326
  sheet: -1.43 (0.63), residues: 68
  loop : -0.74 (0.55), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 180 
 TYR   0.017   0.001   TYR B 182 
 PHE   0.006   0.001   PHE B 291 
 TRP   0.011   0.001   TRP A 119 
 HIS   0.002   0.000   HIS B  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.11 ( 4670)
  covalent geometry    : angle       0.61838 /  0.29 ( 6336)
  hydrogen bonds       : bond        0.02851 /  2.00 (  255)
  hydrogen bonds       : angle       3.76228 /  2.73 (  753)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 TRP cc_start: 0.5830 (OUTLIER) cc_final: 0.5285 (m-10)
REVERT: A  196 GLN cc_start: 0.8612 (tt0) cc_final: 0.7677 (tm-30)
REVERT: A  199 TYR cc_start: 0.7665 (m-80) cc_final: 0.6863 (m-80)
REVERT: B  199 TYR cc_start: 0.7746 (m-80) cc_final: 0.7094 (m-80)
REVERT: B  257 CYS cc_start: 0.7848 (t) cc_final: 0.6937 (t)
  outliers start: 10
  outliers final: 7
  residues processed: 85
  average time/residue: 0.0563
  time to fit residues: 6.3230
Evaluate side-chains
  83 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ILE
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue  119 TRP
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain B residue   34 TRP
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue  208 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 52 optimal weight:    0.4980
   chunk 56 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 9 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.8384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.229239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.202321 restraints weight = 6402.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.207836 restraints weight = 3843.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.211938 restraints weight = 2571.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.214860 restraints weight = 1842.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.216998 restraints weight = 1389.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.4328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6296
moved from start:          0.4323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4670  Z= 0.121
  Angle     :  0.660  11.819   6336  Z= 0.301
  Chirality :  0.040   0.220    730
  Planarity :  0.004   0.034    798
  Dihedral  :  3.508  17.021    638
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 21.19 %
    Favored  : 76.75 %
  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:  1.24 (0.38), residues: 552
  helix:  2.14 (0.28), residues: 324
  sheet: -1.59 (0.62), residues: 68
  loop : -0.79 (0.54), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 180 
 TYR   0.018   0.001   TYR B 182 
 PHE   0.009   0.001   PHE A 279 
 TRP   0.006   0.001   TRP A 119 
 HIS   0.003   0.001   HIS B  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 4670)
  covalent geometry    : angle       0.65956 /  0.30 ( 6336)
  hydrogen bonds       : bond        0.03145 /  2.19 (  255)
  hydrogen bonds       : angle       3.87947 /  2.84 (  753)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 LEU cc_start: 0.6360 (mm) cc_final: 0.5608 (tp)
REVERT: A  119 TRP cc_start: 0.6093 (OUTLIER) cc_final: 0.5283 (m-10)
REVERT: A  196 GLN cc_start: 0.8678 (tt0) cc_final: 0.7604 (tm-30)
REVERT: A  199 TYR cc_start: 0.7749 (m-80) cc_final: 0.6913 (m-80)
REVERT: B  106 TYR cc_start: 0.6358 (OUTLIER) cc_final: 0.5576 (t80)
REVERT: B  196 GLN cc_start: 0.8646 (tt0) cc_final: 0.7951 (tm-30)
REVERT: B  199 TYR cc_start: 0.7906 (m-80) cc_final: 0.7258 (m-80)
REVERT: B  257 CYS cc_start: 0.8010 (t) cc_final: 0.7179 (t)
  outliers start: 10
  outliers final: 8
  residues processed: 84
  average time/residue: 0.0455
  time to fit residues: 5.1719
Evaluate side-chains
  84 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ILE
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue  119 TRP
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain B residue   10 ILE
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  208 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 47 optimal weight:    0.1980
   chunk 2 optimal weight:    0.7980
   chunk 36 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.1582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 307 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.225878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.199200 restraints weight = 6340.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.204729 restraints weight = 3745.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.208773 restraints weight = 2473.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.211498 restraints weight = 1760.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.213522 restraints weight = 1338.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.4295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6358
moved from start:          0.4531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4670  Z= 0.137
  Angle     :  0.682  10.984   6336  Z= 0.313
  Chirality :  0.041   0.220    730
  Planarity :  0.004   0.034    798
  Dihedral  :  3.634  14.427    638
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 20.78 %
    Favored  : 76.13 %
  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:  1.12 (0.38), residues: 552
  helix:  2.01 (0.29), residues: 324
  sheet: -1.57 (0.63), residues: 68
  loop : -0.77 (0.54), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 197 
 TYR   0.018   0.002   TYR B 182 
 PHE   0.011   0.001   PHE B 279 
 TRP   0.006   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.14 ( 4670)
  covalent geometry    : angle       0.68184 /  0.31 ( 6336)
  hydrogen bonds       : bond        0.03379 /  2.34 (  255)
  hydrogen bonds       : angle       4.03744 /  2.99 (  753)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 662.74 seconds
wall clock time: 12 minutes 7.06 seconds (727.06 seconds total)