Starting phenix.real_space_refine
on Sun Apr  5 03:16:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9x0j_66435/04_2026/9x0j_66435.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9x0j_66435/04_2026/9x0j_66435.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9x0j_66435/04_2026/9x0j_66435.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9x0j_66435/04_2026/9x0j_66435.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9x0j_66435/04_2026/9x0j_66435.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9x0j_66435/04_2026/9x0j_66435.map"
  }
  resolution = 2.57
  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=  -0.001 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1334 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    4011      2.51       5
     N    1143      2.21       5
     O    1327      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6499
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1045
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 150, 1045
          Classifications: {'peptide': 150}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 143}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 167
          Unresolved non-hydrogen angles: 213
          Unresolved non-hydrogen dihedrals: 141
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLU:plan': 6, 'TYR:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 2, 'ASP:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 90
    Chain: "C"
      Number of atoms: 1253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1253
          Classifications: {'peptide': 199}
          Incomplete info: {'truncation_to_alanine': 64}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 183}
          Chain breaks: 4
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 241
          Unresolved non-hydrogen angles: 309
          Unresolved non-hydrogen dihedrals: 208
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'TYR:plan': 6, 'GLU:plan': 6, 'GLN:plan1': 5, 'ARG:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 135
    Chain: "F"
      Number of atoms: 1348
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 219, 1345
          Classifications: {'peptide': 219}
          Incomplete info: {'truncation_to_alanine': 87}
          Link IDs: {'PTRANS': 12, 'TRANS': 206}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 322
          Unresolved non-hydrogen angles: 416
          Unresolved non-hydrogen dihedrals: 272
          Unresolved non-hydrogen chiralities: 33
          Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 6, 'TYR:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 172
      Conformer: "B"
        Number of residues, atoms: 219, 1345
          Classifications: {'peptide': 219}
          Incomplete info: {'truncation_to_alanine': 87}
          Link IDs: {'PTRANS': 12, 'TRANS': 206}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 322
          Unresolved non-hydrogen angles: 416
          Unresolved non-hydrogen dihedrals: 272
          Unresolved non-hydrogen chiralities: 33
          Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 6, 'TYR:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 172
          bond proxies already assigned to first conformer: 1363
    Chain: "E"
      Number of atoms: 1471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1471
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 65}
          Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 204}
          Chain breaks: 2
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 218
          Unresolved non-hydrogen angles: 285
          Unresolved non-hydrogen dihedrals: 186
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'TRP:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 92
    Chain: "B"
      Number of atoms: 1382
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1382
          Classifications: {'peptide': 208}
          Incomplete info: {'truncation_to_alanine': 63}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 196}
          Chain breaks: 3
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 236
          Unresolved non-hydrogen angles: 305
          Unresolved non-hydrogen dihedrals: 195
          Unresolved non-hydrogen chiralities: 23
          Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 5, 'GLU:plan': 2, 'TYR:plan': 3, 'PHE:plan': 2, 'TRP:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 130
  Time building chain proxies: 1.52, per 1000 atoms: 0.23
  Number of scatterers: 6499
  At special positions: 0
  Unit cell: (63.3778, 85.936, 175.095, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      18     16.00
     O    1327      8.00
     N    1143      7.00
     C    4011      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 149 " - pdb=" SG  CYS E 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 134 " - pdb=" SG  CYS B 194 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.61
  Conformation dependent library (CDL) restraints added in 347.1 milliseconds
  

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1844

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 23 sheets defined
      5.7% alpha, 34.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'C' and resid 78 through 82
    Processing helix  chain 'C' and resid 181 through 186
    Processing helix  chain 'F' and resid 62 through 65
    Processing helix  chain 'F' and resid 87 through 91
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.793A  pdb=" N   TYR E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 65
    Processing helix  chain 'E' and resid 194 through 201
      removed outlier: 4.075A  pdb=" N   GLY E 199 " --> pdb=" O   SER E 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 83
    Processing helix  chain 'B' and resid 123 through 128
      removed outlier: 3.546A  pdb=" N   GLY B 128 " --> pdb=" O   GLN B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 187
      removed outlier: 4.115A  pdb=" N   GLU B 187 " --> pdb=" O   LYS B 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 183 through 187'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 124
      removed outlier: 3.783A  pdb=" N   THR A 120 " --> pdb=" O   TYR A 163 " (cutoff:3.500A)
      removed outlier: 5.712A  pdb=" N   LEU A 182 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   PHE A 230 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   VAL A 238 " --> pdb=" O   CYS A 232 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 128
    Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 138
    Processing sheet with id=AA4, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.511A  pdb=" N   ALA C  83 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   TRP C  34 " --> pdb=" O   VAL C  46 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.511A  pdb=" N   ALA C  83 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 20 through 23
      removed outlier: 3.884A  pdb=" N   THR C  73 " --> pdb=" O   SER C  62 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 114 through 116
      removed outlier: 6.278A  pdb=" N   TYR C 172 " --> pdb=" O   ASP C 138 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 130 through 132
    Processing sheet with id=AA9, first strand: chain 'C' and resid 144 through 147
    Processing sheet with id=AB1, first strand: chain 'F' and resid 6 through 7
    Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 12
      removed outlier: 3.505A  pdb=" N   GLN F  99 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ALA F  33 " --> pdb=" O   GLN F  99 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   MET F  34 " --> pdb=" O   ILE F  51 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ARG F  38 " --> pdb=" O   TRP F  47 " (cutoff:3.500A)
      removed outlier: 5.449A  pdb=" N   TRP F  47 " --> pdb=" O   ARG F  38 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 150 through 151
    Processing sheet with id=AB4, first strand: chain 'F' and resid 179 through 183
      removed outlier: 6.486A  pdb=" N   SER F 192 " --> pdb=" O   PRO F 180 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL F 182 " --> pdb=" O   SER F 190 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 6
      removed outlier: 3.509A  pdb=" N   LEU E  83 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.112A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.128A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ASP E  59 " --> pdb=" O   THR E  50 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.793A  pdb=" N   PHE E 111 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 129 through 131
      removed outlier: 3.640A  pdb=" N   CYS E 149 " --> pdb=" O   SER E 189 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   SER E 189 " --> pdb=" O   CYS E 149 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   TYR E 185 " --> pdb=" O   ASP E 153 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 145 through 146
    Processing sheet with id=AC1, first strand: chain 'E' and resid 159 through 162
    Processing sheet with id=AC2, first strand: chain 'B' and resid 4 through 7
      removed outlier: 4.760A  pdb=" N   ASP B  17 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   SER B  77 " --> pdb=" O   ASP B  17 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   VAL B  19 " --> pdb=" O   ILE B  75 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ILE B  75 " --> pdb=" O   VAL B  19 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.536A  pdb=" N   VAL B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   TYR B  49 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 114 through 115
      removed outlier: 4.838A  pdb=" N   SER B 131 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 7.357A  pdb=" N   LEU B 181 " --> pdb=" O   SER B 131 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   VAL B 133 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   LEU B 179 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
      removed outlier: 5.138A  pdb=" N   LEU B 135 " --> pdb=" O   SER B 177 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   SER B 177 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   ASN B 137 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   LEU B 175 " --> pdb=" O   ASN B 137 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 144 through 147

    234 hydrogen bonds defined for protein.
    521 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.90

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2112
        1.33 -     1.45: 1046
        1.45 -     1.57: 3427
        1.57 -     1.69: 0
        1.69 -     1.81: 23
  Bond restraints: 6608
  Sorted by residual:
  bond pdb=" CA  SER A 166 "
       pdb=" CB  SER A 166 "
    ideal  model  delta    sigma   weight residual
    1.533  1.473  0.060 1.82e-02 3.02e+03 1.08e+01
  bond pdb=" CA  SER A 170 "
       pdb=" CB  SER A 170 "
    ideal  model  delta    sigma   weight residual
    1.528  1.484  0.043 1.35e-02 5.49e+03 1.02e+01
  bond pdb=" N   HIS A 168 "
       pdb=" CA  HIS A 168 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.41e-02 5.03e+03 8.13e+00
  bond pdb=" N   SER A 170 "
       pdb=" CA  SER A 170 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.16e-02 7.43e+03 6.06e+00
  bond pdb=" N   GLU A 165 "
       pdb=" CA  GLU A 165 "
    ideal  model  delta    sigma   weight residual
    1.455  1.484 -0.028 1.22e-02 6.72e+03 5.43e+00
  ... (remaining 6603 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 8786
        2.16 -     4.33: 232
        4.33 -     6.49: 16
        6.49 -     8.65: 8
        8.65 -    10.81: 3
  Bond angle restraints: 9045
  Sorted by residual:
  angle pdb=" N   SER A 170 "
        pdb=" CA  SER A 170 "
        pdb=" C   SER A 170 "
      ideal   model   delta    sigma   weight residual
     112.26  104.91    7.35 1.32e+00 5.74e-01 3.10e+01
  angle pdb=" CA  PRO A 169 "
        pdb=" N   PRO A 169 "
        pdb=" CD  PRO A 169 "
      ideal   model   delta    sigma   weight residual
     112.00  105.23    6.77 1.40e+00 5.10e-01 2.34e+01
  angle pdb=" C   TYR B 140 "
        pdb=" N   PRO B 141 "
        pdb=" CA  PRO B 141 "
      ideal   model   delta    sigma   weight residual
     127.00  137.81  -10.81 2.40e+00 1.74e-01 2.03e+01
  angle pdb=" C   HIS A 168 "
        pdb=" CA  HIS A 168 "
        pdb=" CB  HIS A 168 "
      ideal   model   delta    sigma   weight residual
     110.17  118.57   -8.40 1.97e+00 2.58e-01 1.82e+01
  angle pdb=" C   TYR B 140 "
        pdb=" N   PRO B 141 "
        pdb=" CD  PRO B 141 "
      ideal   model   delta    sigma   weight residual
     120.60  111.25    9.35 2.20e+00 2.07e-01 1.81e+01
  ... (remaining 9040 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.10: 3595
       15.10 -    30.19: 248
       30.19 -    45.29: 46
       45.29 -    60.39: 7
       60.39 -    75.49: 13
  Dihedral angle restraints: 3909
    sinusoidal: 1056
      harmonic: 2853
  Sorted by residual:
  dihedral pdb=" CB  CYS E 149 "
           pdb=" SG  CYS E 149 "
           pdb=" SG  CYS E 205 "
           pdb=" CB  CYS E 205 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.75  -69.75     1      1.00e+01 1.00e-02 6.28e+01
  dihedral pdb=" CB  CYS B 134 "
           pdb=" SG  CYS B 134 "
           pdb=" SG  CYS B 194 "
           pdb=" CB  CYS B 194 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  149.43  -56.43     1      1.00e+01 1.00e-02 4.29e+01
  dihedral pdb=" CB  CYS F  22 "
           pdb=" SG  CYS F  22 "
           pdb=" SG  CYS F  96 "
           pdb=" CB  CYS F  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.77  -45.77     1      1.00e+01 1.00e-02 2.90e+01
  ... (remaining 3906 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 898
       0.058 -    0.116: 151
       0.116 -    0.174: 24
       0.174 -    0.232: 2
       0.232 -    0.289: 5
  Chirality restraints: 1080
  Sorted by residual:
  chirality pdb=" CA  GLU A 165 "
            pdb=" N   GLU A 165 "
            pdb=" C   GLU A 165 "
            pdb=" CB  GLU A 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.10e+00
  chirality pdb=" CA  PRO A 169 "
            pdb=" N   PRO A 169 "
            pdb=" C   PRO A 169 "
            pdb=" CB  PRO A 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.99   -0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  HIS A 168 "
            pdb=" N   HIS A 168 "
            pdb=" C   HIS A 168 "
            pdb=" CB  HIS A 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.71e+00
  ... (remaining 1077 not shown)

  Planarity restraints: 1199
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 165 "   -0.027 2.00e-02 2.50e+03   5.40e-02 2.92e+01
        pdb=" C   GLU A 165 "    0.093 2.00e-02 2.50e+03
        pdb=" O   GLU A 165 "   -0.035 2.00e-02 2.50e+03
        pdb=" N   SER A 166 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU F 161 "    0.068 5.00e-02 4.00e+02   1.05e-01 1.75e+01
        pdb=" N   PRO F 162 "   -0.181 5.00e-02 4.00e+02
        pdb=" CA  PRO F 162 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO F 162 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F 214 "   -0.044 5.00e-02 4.00e+02   6.65e-02 7.08e+00
        pdb=" N   PRO F 215 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO F 215 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO F 215 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 1196 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1146
        2.76 -     3.30: 6515
        3.30 -     3.83: 10429
        3.83 -     4.37: 11373
        4.37 -     4.90: 19690
  Nonbonded interactions: 49153
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 122 "
            pdb=" OH  TYR A 163 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   THR E  28 "
            pdb=" OG  SER E  31 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   SER E 136 "
            pdb=" OG1 THR E 140 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" OG  SER C  64 "
            pdb=" O   THR C  71 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" N   GLY F  15 "
            pdb=" O   LEU F  86 "
     model   vdw
     2.354 3.120
  ... (remaining 49148 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.150
  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:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.720
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
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   0.060   6613  Z= 0.236
  Angle     :  0.844  10.815   9055  Z= 0.493
  Chirality :  0.048   0.289   1080
  Planarity :  0.007   0.105   1199
  Dihedral  : 12.194  75.485   2050
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.87 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 13.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.12 (0.27), residues: 962
  helix: -4.93 (0.33), residues: 12
  sheet: -1.36 (0.28), residues: 318
  loop : -1.38 (0.26), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.002   ARG F  19 
 TYR   0.024   0.002   TYR E  32 
 PHE   0.020   0.002   PHE E 131 
 TRP   0.010   0.002   TRP F 116 
 HIS   0.005   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 6608)
  covalent geometry    : angle       0.84381 ( 9045)
  SS BOND              : bond        0.00368 (    5)
  SS BOND              : angle       1.30870 (   10)
  hydrogen bonds       : bond        0.27025 (  223)
  hydrogen bonds       : angle      11.52246 (  521)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.255 
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: symmetry clash
   revert: symmetry clash
REVERT: A  210 LYS cc_start: 0.7246 (mtpp) cc_final: 0.6824 (mppt)
REVERT: F   77 ASN cc_start: 0.6283 (t0) cc_final: 0.5920 (t0)
REVERT: E    3 GLN cc_start: 0.7744 (mm110) cc_final: 0.7321 (mm-40)
REVERT: E   88 SER cc_start: 0.8770 (m) cc_final: 0.8550 (p)
REVERT: B    2 ILE cc_start: 0.8785 (mm) cc_final: 0.8347 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.5256
  time to fit residues: 93.2561
Evaluate side-chains
  124 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:   30.0000
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 222 ASN
C 169 ASN
E   6 GLN
B 147 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.088404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.080827 restraints weight = 32805.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.4120 rms_B_bonded: 3.70
r_work: 0.4045 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4040
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4040 r_free = 0.4040    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4040 r_free = 0.4040    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4040
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6613  Z= 0.195
  Angle     :  0.809  11.409   9055  Z= 0.415
  Chirality :  0.047   0.184   1080
  Planarity :  0.007   0.086   1199
  Dihedral  :  6.147  34.139   1022
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.49 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.38 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.28), residues: 962
  helix: -2.60 (0.77), residues: 6
  sheet: -1.14 (0.27), residues: 345
  loop : -0.96 (0.27), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG F  19 
 TYR   0.024   0.002   TYR B 186 
 PHE   0.027   0.002   PHE E 131 
 TRP   0.011   0.001   TRP F  36 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 6608)
  covalent geometry    : angle       0.80813 ( 9045)
  SS BOND              : bond        0.00496 (    5)
  SS BOND              : angle       1.33966 (   10)
  hydrogen bonds       : bond        0.04440 (  223)
  hydrogen bonds       : angle       8.02716 (  521)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 154
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 LYS cc_start: 0.7537 (mtpp) cc_final: 0.7260 (mppt)
REVERT: C   92 ASP cc_start: 0.8187 (p0) cc_final: 0.7853 (p0)
REVERT: C  129 LYS cc_start: 0.7021 (tttt) cc_final: 0.6821 (ptmt)
REVERT: C  178 LEU cc_start: 0.7213 (tm) cc_final: 0.7003 (mp)
REVERT: F   56 GLN cc_start: 0.8282 (tp-100) cc_final: 0.8052 (tp-100)
REVERT: B  106 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8035 (pp)
  outliers start: 13
  outliers final: 7
  residues processed: 159
  average time/residue: 0.5136
  time to fit residues: 85.7379
Evaluate side-chains
  129 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 121
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  134 CYS
Chi-restraints excluded: chain F residue  115 TYR
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  153 ASP
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  185 ASP
Chi-restraints excluded: chain B residue  207 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0870
   chunk 69 optimal weight:    9.9990
   chunk 66 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    1.3762

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

Flipped N/Q/H residues before XYZ refinement:
C 169 ASN
F  77 ASN
F  82 GLN
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 147 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.087260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.079873 restraints weight = 32088.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.4084 rms_B_bonded: 3.40
r_work: 0.4009 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4025
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4025 r_free = 0.4025    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4025 r_free = 0.4025    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4025
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.3376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6613  Z= 0.214
  Angle     :  0.810  10.218   9055  Z= 0.414
  Chirality :  0.046   0.170   1080
  Planarity :  0.006   0.076   1199
  Dihedral  :  5.936  29.263   1022
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.32 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 21.09 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.28), residues: 962
  helix: -4.42 (0.43), residues: 6
  sheet: -1.30 (0.27), residues: 342
  loop : -0.94 (0.27), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  19 
 TYR   0.023   0.002   TYR B 186 
 PHE   0.027   0.002   PHE E 131 
 TRP   0.009   0.001   TRP F  36 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 6608)
  covalent geometry    : angle       0.80889 ( 9045)
  SS BOND              : bond        0.00518 (    5)
  SS BOND              : angle       1.37941 (   10)
  hydrogen bonds       : bond        0.04254 (  223)
  hydrogen bonds       : angle       7.57840 (  521)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   85 TYR cc_start: 0.7340 (m-80) cc_final: 0.6945 (m-80)
REVERT: C   92 ASP cc_start: 0.8068 (p0) cc_final: 0.7720 (p0)
REVERT: F   56 GLN cc_start: 0.8266 (tp-100) cc_final: 0.8035 (tp-100)
REVERT: F  227 LYS cc_start: 0.6370 (tmtt) cc_final: 0.5640 (ptmt)
REVERT: B  106 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8051 (pp)
REVERT: B  185 ASP cc_start: 0.6015 (OUTLIER) cc_final: 0.5570 (m-30)
  outliers start: 14
  outliers final: 6
  residues processed: 136
  average time/residue: 0.5130
  time to fit residues: 73.3232
Evaluate side-chains
  125 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  185 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 30 optimal weight:    7.9990
   chunk 32 optimal weight:    0.0030
   chunk 21 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0170
   chunk 1 optimal weight:    6.9990
   chunk 55 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.5432

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 245 ASN
A 262 ASN
C 169 ASN
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 147 GLN
B 160 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.088395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.080822 restraints weight = 32467.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.4109 rms_B_bonded: 3.76
r_work: 0.4041 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4061 r_free = 0.4061    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4061 r_free = 0.4061    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.3852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6613  Z= 0.144
  Angle     :  0.774  11.160   9055  Z= 0.386
  Chirality :  0.045   0.158   1080
  Planarity :  0.006   0.062   1199
  Dihedral  :  5.301  24.651   1022
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.52 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 22.03 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.28), residues: 962
  helix: -4.24 (0.61), residues: 12
  sheet: -1.28 (0.26), residues: 353
  loop : -0.71 (0.28), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E  67 
 TYR   0.016   0.001   TYR B 186 
 PHE   0.011   0.001   PHE E  29 
 TRP   0.015   0.001   TRP B  35 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6608)
  covalent geometry    : angle       0.77351 ( 9045)
  SS BOND              : bond        0.00401 (    5)
  SS BOND              : angle       1.06125 (   10)
  hydrogen bonds       : bond        0.03483 (  223)
  hydrogen bonds       : angle       6.88564 (  521)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   92 ASP cc_start: 0.7965 (p0) cc_final: 0.7644 (p0)
REVERT: B  106 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8043 (pp)
  outliers start: 12
  outliers final: 4
  residues processed: 132
  average time/residue: 0.5064
  time to fit residues: 70.3421
Evaluate side-chains
  118 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 113
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain F residue  115 TYR
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  146 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    0.0050
   chunk 35 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 93 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    1.4798

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

Flipped N/Q/H residues before XYZ refinement:
** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 169 ASN
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.085218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.078293 restraints weight = 33192.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.4101 rms_B_bonded: 3.34
r_work: 0.4036 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4033
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4033 r_free = 0.4033    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4033 r_free = 0.4033    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4033
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.4135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6613  Z= 0.222
  Angle     :  0.838  10.534   9055  Z= 0.428
  Chirality :  0.045   0.173   1080
  Planarity :  0.006   0.058   1199
  Dihedral  :  5.654  24.890   1022
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.32 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 23.92 %
    Favored  : 73.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.28), residues: 962
  helix:  None (None), residues: 0
  sheet: -1.27 (0.26), residues: 359
  loop : -0.85 (0.27), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  87 
 TYR   0.024   0.002   TYR B 186 
 PHE   0.012   0.001   PHE B  71 
 TRP   0.008   0.001   TRP C 185 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 6608)
  covalent geometry    : angle       0.83777 ( 9045)
  SS BOND              : bond        0.00481 (    5)
  SS BOND              : angle       1.24182 (   10)
  hydrogen bonds       : bond        0.03831 (  223)
  hydrogen bonds       : angle       6.84807 (  521)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: C   92 ASP cc_start: 0.7981 (p0) cc_final: 0.7604 (p0)
REVERT: B  106 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8142 (pp)
REVERT: B  185 ASP cc_start: 0.5693 (OUTLIER) cc_final: 0.5193 (m-30)
  outliers start: 16
  outliers final: 10
  residues processed: 137
  average time/residue: 0.5175
  time to fit residues: 74.3472
Evaluate side-chains
  125 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain C residue   21 THR
Chi-restraints excluded: chain F residue  115 TYR
Chi-restraints excluded: chain E residue   60 TYR
Chi-restraints excluded: chain E residue  179 LEU
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain B residue  138 ASN
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  185 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 68 optimal weight:    6.9990
   chunk 66 optimal weight:    5.9990
   chunk 1 optimal weight:    7.9990
   chunk 78 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0050
   chunk 50 optimal weight:    0.0010
   chunk 2 optimal weight:    3.9990
   chunk 79 optimal weight:    0.7980
   chunk 18 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    1.1002

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

Flipped N/Q/H residues before XYZ refinement:
A 245 ASN
A 262 ASN
C 169 ASN
E 180 GLN
B  27 GLN
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.087011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.079266 restraints weight = 32187.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.4091 rms_B_bonded: 3.38
r_work: 0.4032 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.4032
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4049 r_free = 0.4049    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4049 r_free = 0.4049    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7192
moved from start:          0.4399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6613  Z= 0.189
  Angle     :  0.829  10.511   9055  Z= 0.418
  Chirality :  0.044   0.168   1080
  Planarity :  0.006   0.052   1199
  Dihedral  :  5.437  24.139   1022
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.76 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 25.99 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.28), residues: 962
  helix:  None (None), residues: 0
  sheet: -1.28 (0.27), residues: 360
  loop : -0.86 (0.27), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 211 
 TYR   0.018   0.001   TYR B 186 
 PHE   0.011   0.001   PHE E 131 
 TRP   0.006   0.001   TRP F  36 
 HIS   0.003   0.001   HIS F 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 6608)
  covalent geometry    : angle       0.82828 ( 9045)
  SS BOND              : bond        0.00412 (    5)
  SS BOND              : angle       1.11228 (   10)
  hydrogen bonds       : bond        0.03510 (  223)
  hydrogen bonds       : angle       6.72364 (  521)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   92 ASP cc_start: 0.8090 (p0) cc_final: 0.7704 (p0)
REVERT: E    3 GLN cc_start: 0.7574 (mm110) cc_final: 0.6776 (mm110)
REVERT: B  106 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8145 (pp)
  outliers start: 14
  outliers final: 5
  residues processed: 131
  average time/residue: 0.4958
  time to fit residues: 68.3653
Evaluate side-chains
  118 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 112
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain C residue   21 THR
Chi-restraints excluded: chain F residue  115 TYR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain B residue  106 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 37 optimal weight:    9.9990
   chunk 25 optimal weight:    7.9990
   chunk 10 optimal weight:    0.7980
   chunk 73 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0570
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    0.9300

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

Flipped N/Q/H residues before XYZ refinement:
** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.086300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.078955 restraints weight = 32661.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.4118 rms_B_bonded: 3.32
r_work: 0.4058 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.4058
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4059
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4059 r_free = 0.4059    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4059 r_free = 0.4059    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4059
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.4674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6613  Z= 0.181
  Angle     :  0.854  10.950   9055  Z= 0.429
  Chirality :  0.044   0.155   1080
  Planarity :  0.005   0.054   1199
  Dihedral  :  5.297  23.869   1022
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.39 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 27.68 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (0.28), residues: 962
  helix:  None (None), residues: 0
  sheet: -1.39 (0.27), residues: 349
  loop : -0.88 (0.27), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 211 
 TYR   0.019   0.002   TYR C  48 
 PHE   0.017   0.001   PHE E 111 
 TRP   0.007   0.001   TRP F  36 
 HIS   0.003   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 6608)
  covalent geometry    : angle       0.85405 ( 9045)
  SS BOND              : bond        0.00386 (    5)
  SS BOND              : angle       1.16285 (   10)
  hydrogen bonds       : bond        0.03342 (  223)
  hydrogen bonds       : angle       6.62145 (  521)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   92 ASP cc_start: 0.8075 (p0) cc_final: 0.7677 (p0)
REVERT: E  131 PHE cc_start: 0.6848 (m-10) cc_final: 0.6376 (m-80)
REVERT: B  106 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8175 (pp)
  outliers start: 9
  outliers final: 9
  residues processed: 126
  average time/residue: 0.5214
  time to fit residues: 69.1835
Evaluate side-chains
  119 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain C residue   21 THR
Chi-restraints excluded: chain F residue  115 TYR
Chi-restraints excluded: chain E residue   59 ASP
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  185 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 64 optimal weight:    0.7980
   chunk 95 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 39 optimal weight:    0.0270
   chunk 61 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    1.1040

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

Flipped N/Q/H residues before XYZ refinement:
** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.100471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.080643 restraints weight = 28817.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.4076 rms_B_bonded: 6.87
r_work: 0.3922 rms_B_bonded: 6.26 restraints_weight: 2.0000
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3922
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3922 r_free = 0.3922    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3922 r_free = 0.3922    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3922
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.4773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6613  Z= 0.194
  Angle     :  0.859  10.968   9055  Z= 0.434
  Chirality :  0.044   0.165   1080
  Planarity :  0.006   0.080   1199
  Dihedral  :  5.352  23.705   1022
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.70 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 27.50 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.75 (0.28), residues: 962
  helix:  None (None), residues: 0
  sheet: -1.57 (0.26), residues: 358
  loop : -0.83 (0.27), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E  87 
 TYR   0.019   0.002   TYR E  60 
 PHE   0.010   0.001   PHE E 131 
 TRP   0.007   0.001   TRP F  36 
 HIS   0.003   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 6608)
  covalent geometry    : angle       0.85837 ( 9045)
  SS BOND              : bond        0.00402 (    5)
  SS BOND              : angle       1.13039 (   10)
  hydrogen bonds       : bond        0.03337 (  223)
  hydrogen bonds       : angle       6.70675 (  521)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   92 ASP cc_start: 0.8766 (p0) cc_final: 0.8417 (p0)
REVERT: F  227 LYS cc_start: 0.6507 (tptt) cc_final: 0.5606 (ptmt)
REVERT: E    3 GLN cc_start: 0.8310 (mm110) cc_final: 0.8107 (mm-40)
REVERT: E  131 PHE cc_start: 0.7936 (m-10) cc_final: 0.7427 (m-80)
REVERT: B  106 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8744 (pp)
  outliers start: 10
  outliers final: 8
  residues processed: 127
  average time/residue: 0.5303
  time to fit residues: 70.6689
Evaluate side-chains
  119 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain C residue   21 THR
Chi-restraints excluded: chain F residue  115 TYR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  185 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 83 optimal weight:    0.9980
   chunk 89 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 169 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.087915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.080458 restraints weight = 31275.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.4117 rms_B_bonded: 3.51
r_work: 0.4041 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4036
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4036 r_free = 0.4036    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4036 r_free = 0.4036    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4036
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.4932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6613  Z= 0.205
  Angle     :  0.916  10.677   9055  Z= 0.461
  Chirality :  0.045   0.163   1080
  Planarity :  0.006   0.075   1199
  Dihedral  :  5.441  24.363   1022
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.22 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 28.06 %
    Favored  : 69.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.28), residues: 962
  helix:  None (None), residues: 0
  sheet: -1.62 (0.26), residues: 358
  loop : -0.85 (0.27), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E  87 
 TYR   0.026   0.002   TYR A 146 
 PHE   0.022   0.001   PHE E  29 
 TRP   0.006   0.001   TRP F  36 
 HIS   0.003   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 6608)
  covalent geometry    : angle       0.91631 ( 9045)
  SS BOND              : bond        0.00400 (    5)
  SS BOND              : angle       1.06561 (   10)
  hydrogen bonds       : bond        0.03377 (  223)
  hydrogen bonds       : angle       6.77741 (  521)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   92 ASP cc_start: 0.8226 (p0) cc_final: 0.7844 (p0)
REVERT: F  227 LYS cc_start: 0.6454 (tptt) cc_final: 0.5606 (ptmt)
  outliers start: 11
  outliers final: 9
  residues processed: 125
  average time/residue: 0.5414
  time to fit residues: 70.8873
Evaluate side-chains
  117 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain C residue   21 THR
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain F residue  115 TYR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  185 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0470
   chunk 74 optimal weight:    0.8980
   chunk 71 optimal weight:   10.0000
   chunk 86 optimal weight:    0.0570
   chunk 80 optimal weight:    4.9990
   chunk 29 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9990
   chunk 75 optimal weight:    6.9990
   chunk 32 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
A 262 ASN
F  56 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.088998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.081499 restraints weight = 30867.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.4134 rms_B_bonded: 3.66
r_work: 0.4065 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4061 r_free = 0.4061    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4061 r_free = 0.4061    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.5078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   6613  Z= 0.170
  Angle     :  0.931  13.028   9055  Z= 0.462
  Chirality :  0.045   0.164   1080
  Planarity :  0.006   0.068   1199
  Dihedral  :  5.204  23.375   1022
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.83 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 29.38 %
    Favored  : 68.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.82 (0.28), residues: 962
  helix: -5.54 (0.21), residues: 6
  sheet: -1.59 (0.26), residues: 371
  loop : -0.82 (0.28), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 211 
 TYR   0.029   0.002   TYR C  48 
 PHE   0.015   0.001   PHE E  29 
 TRP   0.007   0.001   TRP F  36 
 HIS   0.002   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 6608)
  covalent geometry    : angle       0.93057 ( 9045)
  SS BOND              : bond        0.00322 (    5)
  SS BOND              : angle       1.09065 (   10)
  hydrogen bonds       : bond        0.03067 (  223)
  hydrogen bonds       : angle       6.62383 (  521)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   92 ASP cc_start: 0.8228 (p0) cc_final: 0.7834 (p0)
REVERT: E  131 PHE cc_start: 0.7057 (m-10) cc_final: 0.6646 (m-80)
  outliers start: 12
  outliers final: 9
  residues processed: 128
  average time/residue: 0.5215
  time to fit residues: 70.2583
Evaluate side-chains
  123 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain C residue   21 THR
Chi-restraints excluded: chain C residue   29 ASP
Chi-restraints excluded: chain F residue   56 GLN
Chi-restraints excluded: chain F residue  115 TYR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  185 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 74 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   chunk 29 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
F  56 GLN
** F 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.088328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.080250 restraints weight = 31954.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.4120 rms_B_bonded: 3.44
r_work: 0.4059 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.4059
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4059
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4059 r_free = 0.4059    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4059 r_free = 0.4059    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4059
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
moved from start:          0.5085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.309   6613  Z= 0.415
  Angle     :  1.366  59.199   9055  Z= 0.732
  Chirality :  0.047   0.421   1080
  Planarity :  0.008   0.205   1199
  Dihedral  :  5.201  23.268   1022
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 16.64
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.04 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 30.32 %
    Favored  : 67.98 %
  Cbeta Deviations :  0.22 %
  Peptide Plane:
    Cis-proline     : 13.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.81 (0.28), residues: 962
  helix: -5.54 (0.21), residues: 6
  sheet: -1.58 (0.26), residues: 370
  loop : -0.82 (0.28), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.002   ARG F 110 
 TYR   0.028   0.002   TYR C  48 
 PHE   0.008   0.001   PHE E 111 
 TRP   0.007   0.001   TRP F  36 
 HIS   0.003   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00849 ( 6608)
  covalent geometry    : angle       1.36666 ( 9045)
  SS BOND              : bond        0.00300 (    5)
  SS BOND              : angle       1.09154 (   10)
  hydrogen bonds       : bond        0.03077 (  223)
  hydrogen bonds       : angle       6.62795 (  521)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3268.02 seconds
wall clock time: 56 minutes 3.98 seconds (3363.98 seconds total)