Starting phenix.real_space_refine
on Thu Sep 18 16:19:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k49_62050/09_2025/9k49_62050.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k49_62050/09_2025/9k49_62050.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k49_62050/09_2025/9k49_62050.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k49_62050/09_2025/9k49_62050.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k49_62050/09_2025/9k49_62050.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k49_62050/09_2025/9k49_62050.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    5920      2.51       5
     N    1559      2.21       5
     O    1605      1.98       5
     H    9352      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18473
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3457
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 3457
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 5, 'TRANS': 212}
    Chain: "B"
      Number of atoms: 3438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 3438
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 5, 'TRANS': 211}
    Chain: "C"
      Number of atoms: 3457
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 3457
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 5, 'TRANS': 212}
    Chain: "D"
      Number of atoms: 3476
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 3476
          Classifications: {'peptide': 219}
          Link IDs: {'PTRANS': 5, 'TRANS': 213}
    Chain: "E"
      Number of atoms: 3457
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 3457
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 5, 'TRANS': 212}
    Chain: "F"
      Number of atoms: 350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 350
          Classifications: {'peptide': 21}
          Link IDs: {'PTRANS': 1, 'TRANS': 19}
    Chain: "G"
      Number of atoms: 391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 391
          Classifications: {'peptide': 23}
          Link IDs: {'PTRANS': 1, 'TRANS': 21}
    Chain: "H"
      Number of atoms: 447
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 447
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
  Time building chain proxies: 3.84, per 1000 atoms: 0.21
  Number of scatterers: 18473
  At special positions: 0
  Unit cell: (85.068, 90.906, 114.258, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      37     16.00
     O    1605      8.00
     N    1559      7.00
     C    5920      6.00
     H    9352      1.00
    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: 1.78
  Conformation dependent library (CDL) restraints added in 646.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2182

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 0 sheets defined
      85.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 59
      removed outlier: 3.912A  pdb=" N   GLU A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA A  51 " --> pdb=" O   ARG A  47 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   LYS A  55 " --> pdb=" O   ALA A  51 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   GLY A  59 " --> pdb=" O   LYS A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 69
    Processing helix  chain 'A' and resid 77 through 98
    Processing helix  chain 'A' and resid 102 through 124
      removed outlier: 3.861A  pdb=" N   GLU A 106 " --> pdb=" O   GLU A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 128
      No H-bonds generated for 'chain 'A' and resid 126 through 128'
    Processing helix  chain 'A' and resid 129 through 135
      removed outlier: 3.555A  pdb=" N   SER A 135 " --> pdb=" O   GLY A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 156
    Processing helix  chain 'A' and resid 164 through 166
      No H-bonds generated for 'chain 'A' and resid 164 through 166'
    Processing helix  chain 'A' and resid 167 through 180
      removed outlier: 3.750A  pdb=" N   THR A 178 " --> pdb=" O   ALA A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 184
    Processing helix  chain 'A' and resid 185 through 222
      removed outlier: 3.638A  pdb=" N   ALA A 215 " --> pdb=" O   GLU A 211 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 56
      removed outlier: 3.754A  pdb=" N   ASN B  43 " --> pdb=" O   THR B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 72
      removed outlier: 3.829A  pdb=" N   GLY B  71 " --> pdb=" O   GLN B  67 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   LYS B  72 " --> pdb=" O   GLU B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 96
      removed outlier: 3.696A  pdb=" N   ILE B  82 " --> pdb=" O   GLY B  78 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLY B  86 " --> pdb=" O   ILE B  82 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   HIS B  94 " --> pdb=" O   PHE B  90 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ALA B  96 " --> pdb=" O   ARG B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 124
      removed outlier: 3.577A  pdb=" N   VAL B 104 " --> pdb=" O   ALA B 100 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   VAL B 105 " --> pdb=" O   PRO B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 159
      Proline residue:  B 138  - end of helix
      removed outlier: 3.657A  pdb=" N   ALA B 158 " --> pdb=" O   ILE B 154 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   VAL B 159 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 220
      removed outlier: 4.517A  pdb=" N   ALA B 177 " --> pdb=" O   GLU B 173 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   THR B 178 " --> pdb=" O   ALA B 174 " (cutoff:3.500A)
      Proline residue:  B 187  - end of helix
      removed outlier: 4.484A  pdb=" N   ASN B 193 " --> pdb=" O   VAL B 189 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   ARG B 194 " --> pdb=" O   MET B 190 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ARG B 198 " --> pdb=" O   ARG B 194 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ARG B 219 " --> pdb=" O   ALA B 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 57
      removed outlier: 3.813A  pdb=" N   ILE C  36 " --> pdb=" O   TRP C  32 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE C  41 " --> pdb=" O   GLN C  37 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   TRP C  57 " --> pdb=" O   GLU C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 72
    Processing helix  chain 'C' and resid 78 through 94
      removed outlier: 3.901A  pdb=" N   ILE C  82 " --> pdb=" O   GLY C  78 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   GLY C  86 " --> pdb=" O   ILE C  82 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   GLU C  89 " --> pdb=" O   SER C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 124
    Processing helix  chain 'C' and resid 126 through 135
      removed outlier: 3.738A  pdb=" N   LEU C 130 " --> pdb=" O   HIS C 126 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLY C 131 " --> pdb=" O   ILE C 127 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   THR C 132 " --> pdb=" O   PRO C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 155
      removed outlier: 3.698A  pdb=" N   ALA C 155 " --> pdb=" O   HIS C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 156 through 158
      No H-bonds generated for 'chain 'C' and resid 156 through 158'
    Processing helix  chain 'C' and resid 167 through 224
      removed outlier: 4.146A  pdb=" N   ALA C 177 " --> pdb=" O   GLU C 173 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   THR C 178 " --> pdb=" O   ALA C 174 " (cutoff:3.500A)
      Proline residue:  C 187  - end of helix
      removed outlier: 4.186A  pdb=" N   ASN C 196 " --> pdb=" O   TYR C 192 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ALA C 215 " --> pdb=" O   GLU C 211 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 14 through 57
      removed outlier: 3.898A  pdb=" N   ARG D  40 " --> pdb=" O   ILE D  36 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ILE D  41 " --> pdb=" O   GLN D  37 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 71
      removed outlier: 4.196A  pdb=" N   GLY D  71 " --> pdb=" O   GLN D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 77 through 96
      removed outlier: 3.612A  pdb=" N   GLN D  81 " --> pdb=" O   THR D  77 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE D  82 " --> pdb=" O   GLY D  78 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLU D  89 " --> pdb=" O   SER D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 124
      removed outlier: 3.618A  pdb=" N   VAL D 104 " --> pdb=" O   ALA D 100 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLU D 121 " --> pdb=" O   ASN D 117 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 157
      Proline residue:  D 138  - end of helix
      removed outlier: 4.463A  pdb=" N   LEU D 142 " --> pdb=" O   PRO D 138 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA D 155 " --> pdb=" O   HIS D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 224
      Proline residue:  D 187  - end of helix
      removed outlier: 4.853A  pdb=" N   ASN D 193 " --> pdb=" O   VAL D 189 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   ARG D 194 " --> pdb=" O   MET D 190 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   VAL D 224 " --> pdb=" O   GLN D 220 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 57
      removed outlier: 3.979A  pdb=" N   LEU E  22 " --> pdb=" O   LYS E  18 " (cutoff:3.500A)
      removed outlier: 5.853A  pdb=" N   LEU E  24 " --> pdb=" O   ILE E  20 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 61 through 69
      removed outlier: 3.557A  pdb=" N   SER E  69 " --> pdb=" O   LEU E  65 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 72 through 76
    Processing helix  chain 'E' and resid 78 through 96
      removed outlier: 3.767A  pdb=" N   ILE E  82 " --> pdb=" O   GLY E  78 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ALA E  96 " --> pdb=" O   ARG E  92 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 103 through 124
    Processing helix  chain 'E' and resid 126 through 155
      Proline residue:  E 138  - end of helix
    Processing helix  chain 'E' and resid 166 through 222
      removed outlier: 4.544A  pdb=" N   GLY E 170 " --> pdb=" O   MET E 166 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ALA E 177 " --> pdb=" O   GLU E 173 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   THR E 178 " --> pdb=" O   ALA E 174 " (cutoff:3.500A)
      Proline residue:  E 187  - end of helix
      removed outlier: 3.805A  pdb=" N   ASN E 193 " --> pdb=" O   VAL E 189 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   ARG E 198 " --> pdb=" O   ARG E 194 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ARG E 219 " --> pdb=" O   ALA E 215 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLN E 220 " --> pdb=" O   ILE E 216 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   PHE E 222 " --> pdb=" O   HIS E 218 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 18 through 31
      removed outlier: 4.023A  pdb=" N   LEU F  22 " --> pdb=" O   ILE F  18 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   ASP F  23 " --> pdb=" O   VAL F  19 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   VAL F  24 " --> pdb=" O   PRO F  20 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LEU F  30 " --> pdb=" O   LEU F  26 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ILE F  31 " --> pdb=" O   VAL F  27 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 18 through 34
      removed outlier: 3.578A  pdb=" N   VAL G  24 " --> pdb=" O   PRO G  20 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   LEU G  25 " --> pdb=" O   LEU G  21 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA G  34 " --> pdb=" O   LEU G  30 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 8 through 33

    738 hydrogen bonds defined for protein.
    2205 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: 4.03

  Time building geometry restraints manager: 2.47 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 9352
        1.03 -     1.23: 2
        1.23 -     1.42: 3865
        1.42 -     1.62: 5355
        1.62 -     1.81: 74
  Bond restraints: 18648
  Sorted by residual:
  bond pdb=" N   TRP H  31 "
       pdb=" CA  TRP H  31 "
    ideal  model  delta    sigma   weight residual
    1.457  1.484 -0.027 1.17e-02 7.31e+03 5.21e+00
  bond pdb=" N   ASP C 207 "
       pdb=" CA  ASP C 207 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.21e-02 6.83e+03 5.07e+00
  bond pdb=" N   ASP C 207 "
       pdb=" H   ASP C 207 "
    ideal  model  delta    sigma   weight residual
    0.860  0.902 -0.042 2.00e-02 2.50e+03 4.43e+00
  bond pdb=" N   LEU H  25 "
       pdb=" H   LEU H  25 "
    ideal  model  delta    sigma   weight residual
    0.860  0.902 -0.042 2.00e-02 2.50e+03 4.36e+00
  bond pdb=" N   TRP H  31 "
       pdb=" H   TRP H  31 "
    ideal  model  delta    sigma   weight residual
    0.860  0.901 -0.041 2.00e-02 2.50e+03 4.20e+00
  ... (remaining 18643 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 32684
        1.66 -     3.32: 914
        3.32 -     4.97: 119
        4.97 -     6.63: 14
        6.63 -     8.29: 5
  Bond angle restraints: 33736
  Sorted by residual:
  angle pdb=" N   ILE A 180 "
        pdb=" CA  ILE A 180 "
        pdb=" C   ILE A 180 "
      ideal   model   delta    sigma   weight residual
     111.91  107.24    4.67 8.90e-01 1.26e+00 2.75e+01
  angle pdb=" N   LEU H  25 "
        pdb=" CA  LEU H  25 "
        pdb=" C   LEU H  25 "
      ideal   model   delta    sigma   weight residual
     110.97  105.87    5.10 1.09e+00 8.42e-01 2.19e+01
  angle pdb=" C   ILE E  20 "
        pdb=" N   MET E  21 "
        pdb=" CA  MET E  21 "
      ideal   model   delta    sigma   weight residual
     121.54  129.83   -8.29 1.91e+00 2.74e-01 1.88e+01
  angle pdb=" C   ASP C 207 "
        pdb=" N   ASN C 208 "
        pdb=" CA  ASN C 208 "
      ideal   model   delta    sigma   weight residual
     120.29  125.34   -5.05 1.42e+00 4.96e-01 1.26e+01
  angle pdb=" N   VAL A 167 "
        pdb=" CA  VAL A 167 "
        pdb=" C   VAL A 167 "
      ideal   model   delta    sigma   weight residual
     111.91  108.75    3.16 8.90e-01 1.26e+00 1.26e+01
  ... (remaining 33731 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.09: 7344
       17.09 -    34.19: 884
       34.19 -    51.28: 292
       51.28 -    68.38: 125
       68.38 -    85.47: 16
  Dihedral angle restraints: 8661
    sinusoidal: 4662
      harmonic: 3999
  Sorted by residual:
  dihedral pdb=" CA  GLN D  70 "
           pdb=" C   GLN D  70 "
           pdb=" N   GLY D  71 "
           pdb=" CA  GLY D  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.57   25.43     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  PRO A 128 "
           pdb=" C   PRO A 128 "
           pdb=" N   PHE A 129 "
           pdb=" CA  PHE A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.66   23.34     0      5.00e+00 4.00e-02 2.18e+01
  dihedral pdb=" CA  PRO D 138 "
           pdb=" C   PRO D 138 "
           pdb=" N   TYR D 139 "
           pdb=" CA  TYR D 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.50   19.50     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 8658 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1150
       0.041 -    0.081: 236
       0.081 -    0.122: 65
       0.122 -    0.163: 5
       0.163 -    0.203: 3
  Chirality restraints: 1459
  Sorted by residual:
  chirality pdb=" CB  THR D 214 "
            pdb=" CA  THR D 214 "
            pdb=" OG1 THR D 214 "
            pdb=" CG2 THR D 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CB  THR E  39 "
            pdb=" CA  THR E  39 "
            pdb=" OG1 THR E  39 "
            pdb=" CG2 THR E  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 9.37e-01
  chirality pdb=" CG  LEU G  30 "
            pdb=" CB  LEU G  30 "
            pdb=" CD1 LEU G  30 "
            pdb=" CD2 LEU G  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.15e-01
  ... (remaining 1456 not shown)

  Planarity restraints: 2711
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET E  21 "   -0.015 2.00e-02 2.50e+03   2.96e-02 8.77e+00
        pdb=" C   MET E  21 "    0.051 2.00e-02 2.50e+03
        pdb=" O   MET E  21 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LEU E  22 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE E  20 "   -0.012 2.00e-02 2.50e+03   2.52e-02 6.35e+00
        pdb=" C   ILE E  20 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ILE E  20 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   MET E  21 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE H  30 "   -0.011 2.00e-02 2.50e+03   2.32e-02 5.37e+00
        pdb=" C   ILE H  30 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ILE H  30 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   TRP H  31 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 2708 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 2079
        2.24 -     2.83: 40544
        2.83 -     3.42: 49312
        3.42 -     4.01: 61788
        4.01 -     4.60: 96939
  Nonbonded interactions: 250662
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C 106 "
            pdb=" H   GLU C 106 "
     model   vdw
     1.653 2.450
  nonbonded pdb=" O   THR C 163 "
            pdb="HE21 GLN C 165 "
     model   vdw
     1.722 2.450
  nonbonded pdb=" OD1 ASN B 208 "
            pdb="HH11 ARG C 113 "
     model   vdw
     1.726 2.450
  nonbonded pdb=" O   ALA B  13 "
            pdb=" HZ1 LYS B  18 "
     model   vdw
     1.730 2.450
  nonbonded pdb=" OE2 GLU C 212 "
            pdb="HH11 ARG D 113 "
     model   vdw
     1.732 2.450
  ... (remaining 250657 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ 
r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid  \ 
9 through 224))
  selection = chain 'B'
  selection = (chain 'C' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ 
r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid  \ 
9 through 224))
  selection = (chain 'D' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ 
r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid  \ 
9 through 224))
  selection = (chain 'E' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ 
r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid  \ 
9 through 224))
}
ncs_group {
  reference = chain 'F'
  selection = (chain 'G' and ((resid 14 and (name N or name CA or name C or name O or name CB  \ 
or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 15 through  \ 
34))
}

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:             1.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.100
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.050
  Process input model:                     18.310
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
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      :  0.004   0.046   9296  Z= 0.170
  Angle     :  0.707   8.290  12572  Z= 0.388
  Chirality :  0.037   0.203   1459
  Planarity :  0.004   0.054   1585
  Dihedral  : 18.220  85.471   3351
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 24.76 %
    Favored  : 73.33 %
  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 aren not related in a simple way.
  whole:  2.11 (0.26), residues: 1145
  helix:  2.18 (0.17), residues: 936
  sheet:  None (None), residues: 0
  loop : -2.45 (0.40), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  73 
 TYR   0.008   0.001   TYR C 206 
 PHE   0.028   0.001   PHE B  83 
 TRP   0.020   0.001   TRP B 147 
 HIS   0.006   0.001   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 9296)
  covalent geometry    : angle       0.70685 (12572)
  hydrogen bonds       : bond        0.10349 (  738)
  hydrogen bonds       : angle       4.69634 ( 2205)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 212
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6421 (pptt)
REVERT: A  164 LEU cc_start: 0.8219 (tp) cc_final: 0.7932 (pt)
REVERT: B   18 LYS cc_start: 0.7768 (mptt) cc_final: 0.7445 (mttm)
REVERT: B  121 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7776 (tm-30)
REVERT: B  201 LYS cc_start: 0.9308 (ttpp) cc_final: 0.8873 (ttmt)
REVERT: C   18 LYS cc_start: 0.7948 (ttpp) cc_final: 0.7470 (ttpp)
REVERT: C  200 ASN cc_start: 0.8643 (t0) cc_final: 0.8431 (t0)
REVERT: C  211 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7560 (tp30)
REVERT: D   25 ILE cc_start: 0.8746 (tp) cc_final: 0.8463 (mt)
REVERT: D   75 ASN cc_start: 0.7502 (p0) cc_final: 0.7188 (p0)
REVERT: E  208 ASN cc_start: 0.7183 (t0) cc_final: 0.6703 (t0)
REVERT: E  212 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7266 (mp0)
  outliers start: 18
  outliers final: 13
  residues processed: 218
  average time/residue: 0.1764
  time to fit residues: 56.4966
Evaluate side-chains
  215 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 199
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TRP
Chi-restraints excluded: chain A residue   67 GLN
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  211 GLU
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue   88 LYS
Chi-restraints excluded: chain D residue  112 MET
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue  212 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
D 208 ASN
D 218 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.150023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.120115 restraints weight = 46922.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.125821 restraints weight = 19378.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.129451 restraints weight = 11498.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.131324 restraints weight = 8459.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.132654 restraints weight = 7165.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.0879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9296  Z= 0.128
  Angle     :  0.511   6.957  12572  Z= 0.281
  Chirality :  0.034   0.125   1459
  Planarity :  0.004   0.045   1585
  Dihedral  :  5.657  51.570   1280
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 23.92 %
    Favored  : 73.33 %
  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 aren not related in a simple way.
  whole:  2.48 (0.26), residues: 1145
  helix:  2.47 (0.17), residues: 944
  sheet:  None (None), residues: 0
  loop : -2.72 (0.38), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 113 
 TYR   0.006   0.001   TYR B  84 
 PHE   0.016   0.001   PHE B 143 
 TRP   0.014   0.001   TRP B 147 
 HIS   0.003   0.000   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 9296)
  covalent geometry    : angle       0.51147 (12572)
  hydrogen bonds       : bond        0.04046 (  738)
  hydrogen bonds       : angle       3.74138 ( 2205)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 199
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6524 (pptt)
REVERT: B   18 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7516 (mttm)
REVERT: B  143 PHE cc_start: 0.8134 (t80) cc_final: 0.7930 (t80)
REVERT: B  201 LYS cc_start: 0.9381 (ttpp) cc_final: 0.8958 (ttmt)
REVERT: C   18 LYS cc_start: 0.7786 (ttpp) cc_final: 0.7318 (ttpp)
REVERT: C  121 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7806 (tm-30)
REVERT: C  200 ASN cc_start: 0.8693 (t0) cc_final: 0.8479 (t0)
REVERT: C  211 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7759 (tp30)
REVERT: D   25 ILE cc_start: 0.8701 (tp) cc_final: 0.8475 (mt)
REVERT: D   75 ASN cc_start: 0.7830 (p0) cc_final: 0.7362 (p0)
REVERT: E   38 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6804 (mmp80)
REVERT: E   52 PHE cc_start: 0.8329 (t80) cc_final: 0.8089 (t80)
REVERT: E  208 ASN cc_start: 0.7599 (t0) cc_final: 0.7151 (t0)
REVERT: E  212 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7280 (mp0)
  outliers start: 26
  outliers final: 14
  residues processed: 214
  average time/residue: 0.1544
  time to fit residues: 49.5139
Evaluate side-chains
  204 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TRP
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain B residue   18 LYS
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  211 GLU
Chi-restraints excluded: chain D residue   88 LYS
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue  212 GLU
Chi-restraints excluded: chain F residue   28 LEU
Chi-restraints excluded: chain G residue   16 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 36 optimal weight:    0.0770
   chunk 51 optimal weight:    1.9990
   chunk 94 optimal weight:    4.9990
   chunk 88 optimal weight:    7.9990
   chunk 61 optimal weight:    3.9990
   chunk 109 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9990
   chunk 72 optimal weight:    6.9990
   overall best weight:    1.0144

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

Flipped N/Q/H residues before XYZ refinement:
D 208 ASN
D 218 HIS
E 218 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.150066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.118985 restraints weight = 47407.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.124782 restraints weight = 20133.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.128393 restraints weight = 12181.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.130573 restraints weight = 9104.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.131566 restraints weight = 7647.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.1026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9296  Z= 0.122
  Angle     :  0.497   6.809  12572  Z= 0.271
  Chirality :  0.034   0.138   1459
  Planarity :  0.003   0.041   1585
  Dihedral  :  4.973  50.874   1264
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 23.28 %
    Favored  : 73.02 %
  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 aren not related in a simple way.
  whole:  2.57 (0.26), residues: 1145
  helix:  2.53 (0.17), residues: 945
  sheet:  None (None), residues: 0
  loop : -2.65 (0.38), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 113 
 TYR   0.008   0.001   TYR B  84 
 PHE   0.014   0.001   PHE B 143 
 TRP   0.016   0.001   TRP B 147 
 HIS   0.003   0.000   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9296)
  covalent geometry    : angle       0.49729 (12572)
  hydrogen bonds       : bond        0.03833 (  738)
  hydrogen bonds       : angle       3.58921 ( 2205)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 195
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 MET cc_start: 0.8564 (mmt) cc_final: 0.8284 (mmp)
REVERT: A  160 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6451 (pptt)
REVERT: B  201 LYS cc_start: 0.9377 (ttpp) cc_final: 0.8954 (ttmt)
REVERT: C   18 LYS cc_start: 0.7801 (ttpp) cc_final: 0.7340 (ttpp)
REVERT: C  116 MET cc_start: 0.8728 (tmm) cc_final: 0.8269 (tmm)
REVERT: C  121 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7880 (tm-30)
REVERT: C  200 ASN cc_start: 0.8700 (t0) cc_final: 0.8490 (t0)
REVERT: C  211 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7750 (tp30)
REVERT: D   25 ILE cc_start: 0.8699 (tp) cc_final: 0.8463 (mt)
REVERT: D   75 ASN cc_start: 0.7827 (p0) cc_final: 0.7307 (p0)
REVERT: E   52 PHE cc_start: 0.8320 (t80) cc_final: 0.8108 (t80)
REVERT: E  212 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7358 (mp0)
  outliers start: 35
  outliers final: 25
  residues processed: 216
  average time/residue: 0.1666
  time to fit residues: 52.9676
Evaluate side-chains
  216 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 188
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TRP
Chi-restraints excluded: chain A residue   67 GLN
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  190 MET
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  211 GLU
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  211 GLU
Chi-restraints excluded: chain D residue   88 LYS
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue  212 GLU
Chi-restraints excluded: chain F residue   28 LEU
Chi-restraints excluded: chain G residue   16 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 67 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0970
   chunk 83 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 30 optimal weight:    0.1980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
D 208 ASN
D 218 HIS
E 117 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.148115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.117647 restraints weight = 47525.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.123298 restraints weight = 19784.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.126905 restraints weight = 11839.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.129025 restraints weight = 8745.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.130265 restraints weight = 7328.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.1265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9296  Z= 0.132
  Angle     :  0.502   8.196  12572  Z= 0.275
  Chirality :  0.034   0.160   1459
  Planarity :  0.004   0.039   1585
  Dihedral  :  4.959  50.547   1264
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 22.43 %
    Favored  : 73.02 %
  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 aren not related in a simple way.
  whole:  2.62 (0.26), residues: 1145
  helix:  2.52 (0.17), residues: 947
  sheet:  None (None), residues: 0
  loop : -2.48 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 113 
 TYR   0.007   0.001   TYR B  84 
 PHE   0.012   0.001   PHE B 209 
 TRP   0.016   0.001   TRP B 147 
 HIS   0.003   0.000   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9296)
  covalent geometry    : angle       0.50218 (12572)
  hydrogen bonds       : bond        0.03733 (  738)
  hydrogen bonds       : angle       3.51892 ( 2205)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 196
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 MET cc_start: 0.8556 (mmt) cc_final: 0.8291 (mmp)
REVERT: A  160 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6427 (pptt)
REVERT: B   18 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7500 (mttm)
REVERT: B  201 LYS cc_start: 0.9379 (ttpp) cc_final: 0.8954 (ttmt)
REVERT: C   18 LYS cc_start: 0.7821 (ttpp) cc_final: 0.7359 (ttpp)
REVERT: C  116 MET cc_start: 0.8749 (tmm) cc_final: 0.8286 (tmm)
REVERT: C  121 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7985 (tm-30)
REVERT: C  200 ASN cc_start: 0.8720 (t0) cc_final: 0.8506 (t0)
REVERT: D   25 ILE cc_start: 0.8713 (tp) cc_final: 0.8482 (mt)
REVERT: D   75 ASN cc_start: 0.7807 (p0) cc_final: 0.7296 (p0)
REVERT: E   53 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8079 (mm-30)
REVERT: E  212 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7349 (mp0)
REVERT: F   30 LEU cc_start: 0.8369 (mt) cc_final: 0.8115 (mt)
  outliers start: 43
  outliers final: 30
  residues processed: 222
  average time/residue: 0.1689
  time to fit residues: 54.6298
Evaluate side-chains
  217 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 184
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TRP
Chi-restraints excluded: chain A residue   67 GLN
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain B residue   18 LYS
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  211 GLU
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   88 LYS
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  217 LEU
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   99 HIS
Chi-restraints excluded: chain E residue  133 VAL
Chi-restraints excluded: chain E residue  176 ILE
Chi-restraints excluded: chain E residue  208 ASN
Chi-restraints excluded: chain E residue  212 GLU
Chi-restraints excluded: chain F residue   28 LEU
Chi-restraints excluded: chain G residue   16 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 93 optimal weight:    0.0040
   chunk 24 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.7596

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

Flipped N/Q/H residues before XYZ refinement:
** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 208 ASN
E 117 ASN
E 218 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.148625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.118814 restraints weight = 47289.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.124342 restraints weight = 20126.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.127845 restraints weight = 12158.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.129745 restraints weight = 9030.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.131188 restraints weight = 7667.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.1366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9296  Z= 0.112
  Angle     :  0.488   8.376  12572  Z= 0.265
  Chirality :  0.034   0.172   1459
  Planarity :  0.003   0.037   1585
  Dihedral  :  4.738  50.338   1261
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 23.28 %
    Favored  : 72.49 %
  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 aren not related in a simple way.
  whole:  2.74 (0.26), residues: 1145
  helix:  2.59 (0.17), residues: 948
  sheet:  None (None), residues: 0
  loop : -2.38 (0.40), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 113 
 TYR   0.007   0.001   TYR B  84 
 PHE   0.016   0.001   PHE B 143 
 TRP   0.020   0.001   TRP B 147 
 HIS   0.002   0.000   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 9296)
  covalent geometry    : angle       0.48820 (12572)
  hydrogen bonds       : bond        0.03648 (  738)
  hydrogen bonds       : angle       3.42760 ( 2205)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 191
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6422 (pptt)
REVERT: A  164 LEU cc_start: 0.8184 (tp) cc_final: 0.7940 (pt)
REVERT: A  180 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8249 (tt)
REVERT: B   18 LYS cc_start: 0.7737 (mptt) cc_final: 0.7386 (mttm)
REVERT: B  201 LYS cc_start: 0.9376 (ttpp) cc_final: 0.8956 (ttmt)
REVERT: C   18 LYS cc_start: 0.7763 (ttpp) cc_final: 0.7288 (ttpp)
REVERT: C  116 MET cc_start: 0.8771 (tmm) cc_final: 0.8049 (tmm)
REVERT: C  200 ASN cc_start: 0.8709 (t0) cc_final: 0.8493 (t0)
REVERT: C  211 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8171 (tp30)
REVERT: D   25 ILE cc_start: 0.8716 (tp) cc_final: 0.8484 (mt)
REVERT: D   75 ASN cc_start: 0.7820 (p0) cc_final: 0.7314 (p0)
REVERT: E   53 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8046 (mm-30)
REVERT: E  212 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7366 (mp0)
REVERT: F   30 LEU cc_start: 0.8440 (mt) cc_final: 0.8193 (mt)
  outliers start: 40
  outliers final: 28
  residues processed: 216
  average time/residue: 0.1722
  time to fit residues: 54.9386
Evaluate side-chains
  216 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 185
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   57 TRP
Chi-restraints excluded: chain A residue   67 GLN
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue   88 LYS
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  217 LEU
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   99 HIS
Chi-restraints excluded: chain E residue  133 VAL
Chi-restraints excluded: chain E residue  176 ILE
Chi-restraints excluded: chain E residue  208 ASN
Chi-restraints excluded: chain E residue  212 GLU
Chi-restraints excluded: chain F residue   28 LEU
Chi-restraints excluded: chain G residue   16 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0370
   chunk 92 optimal weight:    9.9990
   chunk 11 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0980
   chunk 110 optimal weight:    7.9990
   chunk 66 optimal weight:    0.7980
   chunk 27 optimal weight:    0.2980
   overall best weight:    0.3658

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

Flipped N/Q/H residues before XYZ refinement:
** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 208 ASN
E 117 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.149657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.119764 restraints weight = 46902.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.125324 restraints weight = 20040.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.128834 restraints weight = 12126.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.130504 restraints weight = 9039.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.132111 restraints weight = 7789.396|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.068   9296  Z= 0.106
  Angle     :  0.479   7.795  12572  Z= 0.259
  Chirality :  0.034   0.187   1459
  Planarity :  0.003   0.038   1585
  Dihedral  :  4.700  50.349   1261
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 23.60 %
    Favored  : 72.28 %
  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 aren not related in a simple way.
  whole:  2.84 (0.26), residues: 1145
  helix:  2.65 (0.17), residues: 948
  sheet:  None (None), residues: 0
  loop : -2.31 (0.40), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  73 
 TYR   0.010   0.001   TYR E  66 
 PHE   0.008   0.001   PHE D  52 
 TRP   0.017   0.001   TRP B 147 
 HIS   0.003   0.000   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 9296)
  covalent geometry    : angle       0.47896 (12572)
  hydrogen bonds       : bond        0.03594 (  738)
  hydrogen bonds       : angle       3.35028 ( 2205)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 194
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6364 (pptt)
REVERT: A  164 LEU cc_start: 0.8156 (tp) cc_final: 0.7934 (pt)
REVERT: A  180 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8218 (tt)
REVERT: B   18 LYS cc_start: 0.7667 (mptt) cc_final: 0.7330 (mttm)
REVERT: B  165 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7377 (tm-30)
REVERT: B  201 LYS cc_start: 0.9365 (ttpp) cc_final: 0.8939 (ttmt)
REVERT: C   18 LYS cc_start: 0.7790 (ttpp) cc_final: 0.7342 (ttpp)
REVERT: C  200 ASN cc_start: 0.8705 (t0) cc_final: 0.8491 (t0)
REVERT: C  211 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8137 (tp30)
REVERT: D   25 ILE cc_start: 0.8722 (tp) cc_final: 0.8486 (mt)
REVERT: D   75 ASN cc_start: 0.7772 (p0) cc_final: 0.7343 (p0)
REVERT: E   53 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8044 (mm-30)
REVERT: E  212 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7376 (mp0)
REVERT: F   30 LEU cc_start: 0.8408 (mt) cc_final: 0.8184 (mt)
  outliers start: 39
  outliers final: 25
  residues processed: 217
  average time/residue: 0.1748
  time to fit residues: 56.5910
Evaluate side-chains
  215 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 187
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TRP
Chi-restraints excluded: chain A residue   67 GLN
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  190 MET
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  217 LEU
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   99 HIS
Chi-restraints excluded: chain E residue  133 VAL
Chi-restraints excluded: chain E residue  176 ILE
Chi-restraints excluded: chain E residue  208 ASN
Chi-restraints excluded: chain E residue  212 GLU
Chi-restraints excluded: chain F residue   28 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 57 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 84 optimal weight:    9.9990
   chunk 31 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 208 ASN
E 117 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.144952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.114126 restraints weight = 48432.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.119635 restraints weight = 20692.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.123035 restraints weight = 12586.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.125006 restraints weight = 9457.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.126039 restraints weight = 8026.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   9296  Z= 0.222
  Angle     :  0.578   9.348  12572  Z= 0.324
  Chirality :  0.036   0.199   1459
  Planarity :  0.004   0.037   1585
  Dihedral  :  4.712  50.295   1257
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 23.28 %
    Favored  : 71.85 %
  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 aren not related in a simple way.
  whole:  2.33 (0.25), residues: 1145
  helix:  2.30 (0.17), residues: 947
  sheet:  None (None), residues: 0
  loop : -2.41 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  38 
 TYR   0.009   0.001   TYR A 192 
 PHE   0.018   0.002   PHE D  52 
 TRP   0.016   0.002   TRP B 147 
 HIS   0.003   0.001   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 9296)
  covalent geometry    : angle       0.57845 (12572)
  hydrogen bonds       : bond        0.03967 (  738)
  hydrogen bonds       : angle       3.73612 ( 2205)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 184
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LYS cc_start: 0.7444 (tttt) cc_final: 0.6884 (tttm)
REVERT: A  160 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6386 (pptt)
REVERT: B   18 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7434 (mttp)
REVERT: B  201 LYS cc_start: 0.9404 (ttpp) cc_final: 0.8971 (ttmt)
REVERT: C  106 GLU cc_start: 0.8432 (mp0) cc_final: 0.8039 (mp0)
REVERT: C  121 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8063 (tm-30)
REVERT: C  200 ASN cc_start: 0.8762 (t0) cc_final: 0.8552 (t0)
REVERT: D   25 ILE cc_start: 0.8736 (tp) cc_final: 0.8508 (mt)
REVERT: D   75 ASN cc_start: 0.7938 (p0) cc_final: 0.7420 (p0)
REVERT: E   18 LYS cc_start: 0.7754 (tttp) cc_final: 0.6972 (tttm)
REVERT: E   53 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8049 (mm-30)
REVERT: E  212 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7282 (mp0)
REVERT: F   30 LEU cc_start: 0.8403 (mt) cc_final: 0.8157 (mt)
  outliers start: 46
  outliers final: 28
  residues processed: 214
  average time/residue: 0.1741
  time to fit residues: 55.1991
Evaluate side-chains
  209 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 178
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TRP
Chi-restraints excluded: chain A residue   67 GLN
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain B residue   18 LYS
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue   89 GLU
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  217 LEU
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   99 HIS
Chi-restraints excluded: chain E residue  133 VAL
Chi-restraints excluded: chain E residue  176 ILE
Chi-restraints excluded: chain E residue  212 GLU
Chi-restraints excluded: chain F residue   28 LEU
Chi-restraints excluded: chain G residue   16 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 93 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 27 optimal weight:    0.2980
   chunk 35 optimal weight:    7.9990
   chunk 54 optimal weight:    0.7980
   chunk 51 optimal weight:    0.4980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
B 151 HIS
** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 208 ASN
E 117 ASN
E 218 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.148762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.117124 restraints weight = 47506.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.122946 restraints weight = 20632.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.126585 restraints weight = 12669.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.128459 restraints weight = 9531.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.129637 restraints weight = 8188.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9296  Z= 0.115
  Angle     :  0.512   9.292  12572  Z= 0.275
  Chirality :  0.034   0.187   1459
  Planarity :  0.003   0.038   1585
  Dihedral  :  4.762  50.340   1257
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 24.76 %
    Favored  : 71.64 %
  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 aren not related in a simple way.
  whole:  2.66 (0.26), residues: 1145
  helix:  2.52 (0.17), residues: 948
  sheet:  None (None), residues: 0
  loop : -2.34 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 113 
 TYR   0.009   0.001   TYR E  66 
 PHE   0.012   0.001   PHE B 143 
 TRP   0.009   0.001   TRP B 147 
 HIS   0.003   0.000   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 9296)
  covalent geometry    : angle       0.51165 (12572)
  hydrogen bonds       : bond        0.03734 (  738)
  hydrogen bonds       : angle       3.42402 ( 2205)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 190
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.6369 (pptt)
REVERT: A  164 LEU cc_start: 0.8112 (tp) cc_final: 0.7888 (pt)
REVERT: A  180 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8265 (tt)
REVERT: B   18 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7317 (mttm)
REVERT: B  201 LYS cc_start: 0.9380 (ttpp) cc_final: 0.8950 (ttmt)
REVERT: C  200 ASN cc_start: 0.8729 (t0) cc_final: 0.8511 (t0)
REVERT: C  211 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8283 (tp30)
REVERT: D   25 ILE cc_start: 0.8756 (tp) cc_final: 0.8509 (mt)
REVERT: D   75 ASN cc_start: 0.7906 (p0) cc_final: 0.7387 (p0)
REVERT: E   18 LYS cc_start: 0.7709 (tttp) cc_final: 0.6959 (tttm)
REVERT: E   53 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8023 (mm-30)
REVERT: E  212 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7318 (mp0)
REVERT: F   30 LEU cc_start: 0.8453 (mt) cc_final: 0.8220 (mt)
  outliers start: 34
  outliers final: 27
  residues processed: 209
  average time/residue: 0.1601
  time to fit residues: 49.7929
Evaluate side-chains
  217 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 186
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   57 TRP
Chi-restraints excluded: chain A residue   67 GLN
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain B residue   18 LYS
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  190 MET
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue   89 GLU
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  217 LEU
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   99 HIS
Chi-restraints excluded: chain E residue  133 VAL
Chi-restraints excluded: chain E residue  176 ILE
Chi-restraints excluded: chain E residue  212 GLU
Chi-restraints excluded: chain F residue   28 LEU
Chi-restraints excluded: chain G residue   16 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 63 optimal weight:   10.0000
   chunk 71 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 42 optimal weight:   10.0000
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 208 ASN
E 117 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.145573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.114816 restraints weight = 48084.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.120362 restraints weight = 20405.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.123827 restraints weight = 12434.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.125635 restraints weight = 9339.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.126593 restraints weight = 8014.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   9296  Z= 0.177
  Angle     :  0.542   9.873  12572  Z= 0.300
  Chirality :  0.035   0.193   1459
  Planarity :  0.004   0.036   1585
  Dihedral  :  4.798  50.131   1257
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 24.66 %
    Favored  : 71.75 %
  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 aren not related in a simple way.
  whole:  2.46 (0.25), residues: 1145
  helix:  2.39 (0.17), residues: 947
  sheet:  None (None), residues: 0
  loop : -2.38 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 113 
 TYR   0.006   0.001   TYR E 206 
 PHE   0.015   0.001   PHE D  52 
 TRP   0.016   0.001   TRP B 147 
 HIS   0.003   0.000   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 9296)
  covalent geometry    : angle       0.54242 (12572)
  hydrogen bonds       : bond        0.03841 (  738)
  hydrogen bonds       : angle       3.60451 ( 2205)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 186
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6324 (pptt)
REVERT: A  164 LEU cc_start: 0.8138 (tp) cc_final: 0.7914 (pt)
REVERT: B   18 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7369 (mttm)
REVERT: B  201 LYS cc_start: 0.9395 (ttpp) cc_final: 0.8954 (ttmt)
REVERT: C  121 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8114 (tm-30)
REVERT: C  200 ASN cc_start: 0.8769 (t0) cc_final: 0.8554 (t0)
REVERT: C  211 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8301 (tp30)
REVERT: D   25 ILE cc_start: 0.8763 (tp) cc_final: 0.8517 (mt)
REVERT: D   75 ASN cc_start: 0.7926 (p0) cc_final: 0.7403 (p0)
REVERT: E   18 LYS cc_start: 0.7772 (tttp) cc_final: 0.7006 (tttm)
REVERT: E   53 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8024 (mm-30)
REVERT: E  211 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8639 (mm-30)
REVERT: E  212 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7344 (mp0)
REVERT: F   30 LEU cc_start: 0.8484 (mt) cc_final: 0.8252 (mt)
  outliers start: 34
  outliers final: 26
  residues processed: 205
  average time/residue: 0.1587
  time to fit residues: 48.8131
Evaluate side-chains
  213 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 184
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TRP
Chi-restraints excluded: chain A residue   67 GLN
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain B residue   18 LYS
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue   89 GLU
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  217 LEU
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   99 HIS
Chi-restraints excluded: chain E residue  133 VAL
Chi-restraints excluded: chain E residue  176 ILE
Chi-restraints excluded: chain E residue  212 GLU
Chi-restraints excluded: chain F residue   28 LEU
Chi-restraints excluded: chain G residue   16 ILE
Chi-restraints excluded: chain G residue   21 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 105 optimal weight:    0.4980
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 208 ASN
E 117 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.147124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.116743 restraints weight = 47760.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.122346 restraints weight = 19939.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.125881 restraints weight = 11997.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.127489 restraints weight = 8914.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.128897 restraints weight = 7709.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9296  Z= 0.122
  Angle     :  0.510   9.724  12572  Z= 0.277
  Chirality :  0.034   0.190   1459
  Planarity :  0.003   0.037   1585
  Dihedral  :  4.753  50.020   1257
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 25.08 %
    Favored  : 71.75 %
  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 aren not related in a simple way.
  whole:  2.67 (0.26), residues: 1145
  helix:  2.53 (0.17), residues: 947
  sheet:  None (None), residues: 0
  loop : -2.29 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 113 
 TYR   0.007   0.001   TYR E  66 
 PHE   0.011   0.001   PHE D  52 
 TRP   0.015   0.001   TRP B 147 
 HIS   0.004   0.000   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9296)
  covalent geometry    : angle       0.51048 (12572)
  hydrogen bonds       : bond        0.03728 (  738)
  hydrogen bonds       : angle       3.43821 ( 2205)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 188
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6334 (pptt)
REVERT: A  164 LEU cc_start: 0.8151 (tp) cc_final: 0.7941 (pt)
REVERT: A  180 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8292 (tt)
REVERT: B   18 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7318 (mttm)
REVERT: B  201 LYS cc_start: 0.9387 (ttpp) cc_final: 0.8953 (ttmt)
REVERT: C  121 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8124 (tm-30)
REVERT: C  200 ASN cc_start: 0.8737 (t0) cc_final: 0.8519 (t0)
REVERT: C  211 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8333 (tp30)
REVERT: D   25 ILE cc_start: 0.8754 (tp) cc_final: 0.8511 (mt)
REVERT: D   75 ASN cc_start: 0.7939 (p0) cc_final: 0.7495 (p0)
REVERT: E   18 LYS cc_start: 0.7728 (tttp) cc_final: 0.6973 (tttm)
REVERT: E   53 GLU cc_start: 0.8543 (mm-30) cc_final: 0.7979 (mm-30)
REVERT: E  211 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8631 (mm-30)
REVERT: E  212 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7308 (mp0)
REVERT: F   30 LEU cc_start: 0.8445 (mt) cc_final: 0.8217 (mt)
  outliers start: 30
  outliers final: 24
  residues processed: 204
  average time/residue: 0.1650
  time to fit residues: 50.2053
Evaluate side-chains
  212 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 184
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TRP
Chi-restraints excluded: chain A residue   67 GLN
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain B residue   18 LYS
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue   89 GLU
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  217 LEU
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   99 HIS
Chi-restraints excluded: chain E residue  133 VAL
Chi-restraints excluded: chain E residue  176 ILE
Chi-restraints excluded: chain E residue  212 GLU
Chi-restraints excluded: chain F residue   28 LEU
Chi-restraints excluded: chain G residue   16 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 19 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 42 optimal weight:    9.9990
   chunk 109 optimal weight:    6.9990
   chunk 104 optimal weight:    4.9990
   chunk 15 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 208 ASN
E 117 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.145208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.114591 restraints weight = 47901.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.120131 restraints weight = 20193.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.123596 restraints weight = 12244.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.125274 restraints weight = 9174.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.126712 restraints weight = 7912.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   9296  Z= 0.162
  Angle     :  0.534   9.863  12572  Z= 0.294
  Chirality :  0.035   0.199   1459
  Planarity :  0.004   0.036   1585
  Dihedral  :  4.764  49.999   1257
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 24.76 %
    Favored  : 71.85 %
  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 aren not related in a simple way.
  whole:  2.53 (0.25), residues: 1145
  helix:  2.43 (0.17), residues: 949
  sheet:  None (None), residues: 0
  loop : -2.40 (0.41), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 113 
 TYR   0.006   0.001   TYR E 206 
 PHE   0.014   0.001   PHE D  52 
 TRP   0.018   0.001   TRP B 147 
 HIS   0.003   0.000   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 9296)
  covalent geometry    : angle       0.53408 (12572)
  hydrogen bonds       : bond        0.03800 (  738)
  hydrogen bonds       : angle       3.55208 ( 2205)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2934.95 seconds
wall clock time: 50 minutes 36.81 seconds (3036.81 seconds total)