Starting phenix.real_space_refine
on Tue Mar  3 15:55:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xk8_33247/03_2026/7xk8_33247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xk8_33247/03_2026/7xk8_33247.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xk8_33247/03_2026/7xk8_33247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xk8_33247/03_2026/7xk8_33247.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xk8_33247/03_2026/7xk8_33247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xk8_33247/03_2026/7xk8_33247.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    4352      2.51       5
     N    1151      2.21       5
     O    1247      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6796
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "P"
      Number of atoms: 202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 202
          Classifications: {'peptide': 25}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 22}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 2115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2115
          Classifications: {'peptide': 282}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 15, 'TRANS': 266}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 184
          Unresolved non-hydrogen angles: 230
          Unresolved non-hydrogen dihedrals: 162
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'PHE:plan': 7, 'HIS:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 99
    Chain: "A"
      Number of atoms: 1673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1673
          Classifications: {'peptide': 225}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 140
          Unresolved non-hydrogen angles: 165
          Unresolved non-hydrogen dihedrals: 117
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 8, 'ASP:plan': 6, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 77
    Chain: "B"
      Number of atoms: 2432
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2432
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 169
          Unresolved non-hydrogen angles: 204
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ARG:plan': 10, 'GLN:plan1': 4, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 121
    Chain: "C"
      Number of atoms: 373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 373
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 16
  Time building chain proxies: 1.60, per 1000 atoms: 0.24
  Number of scatterers: 6796
  At special positions: 0
  Unit cell: (111.815, 127.49, 85.69, 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      46     16.00
     O    1247      8.00
     N    1151      7.00
     C    4352      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 119 " - pdb=" SG  CYS R 204 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 278.3 milliseconds
  

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1750

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 8 sheets defined
      43.2% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'R' and resid 45 through 72
      Proline residue:  R  54  - end of helix
    Processing helix  chain 'R' and resid 78 through 108
      Proline residue:  R 100  - end of helix
    Processing helix  chain 'R' and resid 115 through 150
    Processing helix  chain 'R' and resid 150 through 156
    Processing helix  chain 'R' and resid 157 through 159
      No H-bonds generated for 'chain 'R' and resid 157 through 159'
    Processing helix  chain 'R' and resid 160 through 184
      Proline residue:  R 180  - end of helix
    Processing helix  chain 'R' and resid 209 through 247
      removed outlier: 4.502A  pdb=" N   LEU R 227 " --> pdb=" O   LEU R 223 " (cutoff:3.500A)
      Proline residue:  R 228  - end of helix
    Processing helix  chain 'R' and resid 259 through 282
    Processing helix  chain 'R' and resid 282 through 292
      removed outlier: 3.987A  pdb=" N   ARG R 288 " --> pdb=" O   PHE R 284 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 299 through 328
      Proline residue:  R 324  - end of helix
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.993A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.624A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   LYS A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 271 through 281
      removed outlier: 4.172A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
    Processing helix  chain 'A' and resid 327 through 352
      removed outlier: 4.264A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 33
    Processing helix  chain 'C' and resid 12 through 21
    Processing helix  chain 'C' and resid 29 through 44
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.747A  pdb=" N   VAL A 185 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS A 197 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU A  36 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.146A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 4.224A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.832A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA B  73 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.863A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ASN B 125 " --> pdb=" O   ARG B 134 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.271A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.988A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.875A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.672A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.802A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    368 hydrogen bonds defined for protein.
    1068 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: 0.68

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1099
        1.31 -     1.44: 1926
        1.44 -     1.56: 3855
        1.56 -     1.69: 0
        1.69 -     1.82: 62
  Bond restraints: 6942
  Sorted by residual:
  bond pdb=" CG  ASN P  25 "
       pdb=" ND2 ASN P  25 "
    ideal  model  delta    sigma   weight residual
    1.328  1.452 -0.124 2.10e-02 2.27e+03 3.46e+01
  bond pdb=" CG  ASN P  25 "
       pdb=" OD1 ASN P  25 "
    ideal  model  delta    sigma   weight residual
    1.231  1.185  0.046 1.90e-02 2.77e+03 5.92e+00
  bond pdb=" C   ASN P  25 "
       pdb=" O   ASN P  25 "
    ideal  model  delta    sigma   weight residual
    1.231  1.184  0.047 2.00e-02 2.50e+03 5.42e+00
  bond pdb=" C   SER P   9 "
       pdb=" N   PRO P  10 "
    ideal  model  delta    sigma   weight residual
    1.334  1.359 -0.025 2.34e-02 1.83e+03 1.12e+00
  bond pdb=" N   PRO R 193 "
       pdb=" CA  PRO R 193 "
    ideal  model  delta    sigma   weight residual
    1.469  1.475 -0.006 7.40e-03 1.83e+04 7.36e-01
  ... (remaining 6937 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 9231
        1.23 -     2.46: 184
        2.46 -     3.68: 41
        3.68 -     4.91: 11
        4.91 -     6.14: 8
  Bond angle restraints: 9475
  Sorted by residual:
  angle pdb=" N   ILE B  33 "
        pdb=" CA  ILE B  33 "
        pdb=" C   ILE B  33 "
      ideal   model   delta    sigma   weight residual
     112.96  109.56    3.40 1.00e+00 1.00e+00 1.16e+01
  angle pdb=" N   GLY R 186 "
        pdb=" CA  GLY R 186 "
        pdb=" C   GLY R 186 "
      ideal   model   delta    sigma   weight residual
     110.80  115.68   -4.88 1.71e+00 3.42e-01 8.15e+00
  angle pdb=" OD1 ASN P  25 "
        pdb=" CG  ASN P  25 "
        pdb=" ND2 ASN P  25 "
      ideal   model   delta    sigma   weight residual
     122.60  119.99    2.61 1.00e+00 1.00e+00 6.82e+00
  angle pdb=" N   THR B 196 "
        pdb=" CA  THR B 196 "
        pdb=" CB  THR B 196 "
      ideal   model   delta    sigma   weight residual
     113.65  110.02    3.63 1.47e+00 4.63e-01 6.11e+00
  angle pdb=" CB  ASN P  25 "
        pdb=" CG  ASN P  25 "
        pdb=" ND2 ASN P  25 "
      ideal   model   delta    sigma   weight residual
     116.40  120.02   -3.62 1.50e+00 4.44e-01 5.81e+00
  ... (remaining 9470 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.57: 3698
       15.57 -    31.14: 291
       31.14 -    46.70: 57
       46.70 -    62.27: 7
       62.27 -    77.84: 1
  Dihedral angle restraints: 4054
    sinusoidal: 1361
      harmonic: 2693
  Sorted by residual:
  dihedral pdb=" CA  PHE R 189 "
           pdb=" C   PHE R 189 "
           pdb=" N   HIS R 190 "
           pdb=" CA  HIS R 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.50   19.50     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CB  CYS R 119 "
           pdb=" SG  CYS R 119 "
           pdb=" SG  CYS R 204 "
           pdb=" CB  CYS R 204 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   65.34   27.66     1      1.00e+01 1.00e-02 1.10e+01
  dihedral pdb=" CA  ASP B  38 "
           pdb=" CB  ASP B  38 "
           pdb=" CG  ASP B  38 "
           pdb=" OD1 ASP B  38 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.44   53.44     1      2.00e+01 2.50e-03 9.71e+00
  ... (remaining 4051 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 756
       0.030 -    0.059: 243
       0.059 -    0.089: 79
       0.089 -    0.119: 44
       0.119 -    0.149: 3
  Chirality restraints: 1125
  Sorted by residual:
  chirality pdb=" CA  THR B 164 "
            pdb=" N   THR B 164 "
            pdb=" C   THR B 164 "
            pdb=" CB  THR B 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.52e-01
  chirality pdb=" CA  ILE R 187 "
            pdb=" N   ILE R 187 "
            pdb=" C   ILE R 187 "
            pdb=" CB  ILE R 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.35e-01
  chirality pdb=" CB  ILE R 184 "
            pdb=" CA  ILE R 184 "
            pdb=" CG1 ILE R 184 "
            pdb=" CG2 ILE R 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.28e-01
  ... (remaining 1122 not shown)

  Planarity restraints: 1203
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R  78 "   -0.019 5.00e-02 4.00e+02   2.88e-02 1.33e+00
        pdb=" N   PRO R  79 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO R  79 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO R  79 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA R 282 "    0.018 5.00e-02 4.00e+02   2.64e-02 1.12e+00
        pdb=" N   PRO R 283 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO R 283 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO R 283 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.015 5.00e-02 4.00e+02   2.26e-02 8.20e-01
        pdb=" N   PRO B 236 "   -0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.013 5.00e-02 4.00e+02
  ... (remaining 1200 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1396
        2.78 -     3.31: 6603
        3.31 -     3.84: 11498
        3.84 -     4.37: 12427
        4.37 -     4.90: 22105
  Nonbonded interactions: 54029
  Sorted by model distance:
  nonbonded pdb=" O   LEU R 289 "
            pdb=" OG  SER R 292 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OG1 THR R  78 "
            pdb=" OD1 ASP A 350 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASN B 110 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.306 3.040
  ... (remaining 54024 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.350
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6270
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      :  0.002   0.124   6944  Z= 0.128
  Angle     :  0.479   6.142   9477  Z= 0.271
  Chirality :  0.038   0.149   1125
  Planarity :  0.003   0.029   1203
  Dihedral  : 11.624  77.838   2301
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.25), residues: 907
  helix:  0.38 (0.24), residues: 371
  sheet: -0.45 (0.38), residues: 154
  loop : -2.23 (0.26), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 251 
 TYR   0.004   0.001   TYR B 289 
 PHE   0.010   0.001   PHE R 291 
 TRP   0.005   0.000   TRP B  99 
 HIS   0.003   0.000   HIS R 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 6942)
  covalent geometry    : angle       0.47857 ( 9475)
  SS BOND              : bond        0.00004 (    1)
  SS BOND              : angle       0.61368 (    2)
  hydrogen bonds       : bond        0.17173 (  368)
  hydrogen bonds       : angle       6.33118 ( 1068)
  Misc. bond           : bond        0.02227 (    1)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  127 GLU cc_start: 0.6423 (tp30) cc_final: 0.6077 (tp30)
REVERT: R  333 ARG cc_start: 0.4321 (pmt170) cc_final: 0.3932 (tpp-160)
REVERT: A    9 ASP cc_start: 0.7360 (t70) cc_final: 0.6993 (t0)
REVERT: B  188 MET cc_start: 0.7046 (mmm) cc_final: 0.6843 (mmm)
REVERT: C   62 ARG cc_start: 0.6621 (mtm-85) cc_final: 0.6392 (mtm110)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.0963
  time to fit residues: 19.8536
Evaluate side-chains
  99 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:   30.0000
   chunk 5 optimal weight:    0.0010
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.2980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
R  43 HIS
R 285 HIS
A  57 HIS
A 294 ASN
A 304 GLN
A 347 ASN
B 340 ASN
C  18 GLN
C  44 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4769 r_free = 0.4769 target = 0.218346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.177263 restraints weight = 7626.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.4388 rms_B_bonded: 3.24
r_work: 0.4049 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.4049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6756
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6944  Z= 0.131
  Angle     :  0.574   7.736   9477  Z= 0.295
  Chirality :  0.042   0.235   1125
  Planarity :  0.003   0.028   1203
  Dihedral  :  3.451  24.373    978
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.33 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.27), residues: 907
  helix:  1.62 (0.26), residues: 373
  sheet: -0.14 (0.40), residues: 141
  loop : -1.76 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 288 
 TYR   0.020   0.001   TYR R 213 
 PHE   0.022   0.001   PHE R 316 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6942)
  covalent geometry    : angle       0.57427 ( 9475)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       1.21750 (    2)
  hydrogen bonds       : bond        0.03585 (  368)
  hydrogen bonds       : angle       4.55818 ( 1068)
  Misc. bond           : bond        0.00130 (    1)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: R  104 TYR cc_start: 0.4043 (m-80) cc_final: 0.3563 (m-80)
REVERT: R  333 ARG cc_start: 0.4958 (pmt170) cc_final: 0.3709 (tpp-160)
REVERT: A    9 ASP cc_start: 0.7246 (t70) cc_final: 0.6888 (t0)
REVERT: A   52 GLN cc_start: 0.6939 (pp30) cc_final: 0.6278 (pp30)
REVERT: B  338 ILE cc_start: 0.6836 (mm) cc_final: 0.6474 (mm)
REVERT: C   62 ARG cc_start: 0.6793 (mtm-85) cc_final: 0.6426 (mtm110)
  outliers start: 13
  outliers final: 5
  residues processed: 130
  average time/residue: 0.0832
  time to fit residues: 14.4472
Evaluate side-chains
  108 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  189 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 83 optimal weight:    0.5980
   chunk 63 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0170
   chunk 59 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.7220

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

Flipped N/Q/H residues before XYZ refinement:
R 285 HIS
A 294 ASN
A 304 GLN
A 347 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4717 r_free = 0.4717 target = 0.212768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.171477 restraints weight = 7601.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.4317 rms_B_bonded: 3.15
r_work: 0.3982 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6872
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6944  Z= 0.136
  Angle     :  0.555   6.816   9477  Z= 0.285
  Chirality :  0.041   0.179   1125
  Planarity :  0.003   0.028   1203
  Dihedral  :  3.684  32.268    978
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 17.46 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.27), residues: 907
  helix:  1.95 (0.27), residues: 376
  sheet: -0.30 (0.40), residues: 150
  loop : -1.48 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 263 
 TYR   0.018   0.001   TYR R 213 
 PHE   0.017   0.001   PHE R 316 
 TRP   0.010   0.001   TRP B 169 
 HIS   0.015   0.001   HIS R 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6942)
  covalent geometry    : angle       0.55496 ( 9475)
  SS BOND              : bond        0.00151 (    1)
  SS BOND              : angle       1.22904 (    2)
  hydrogen bonds       : bond        0.03355 (  368)
  hydrogen bonds       : angle       4.27689 ( 1068)
  Misc. bond           : bond        0.00012 (    1)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: R   49 SER cc_start: 0.5125 (t) cc_final: 0.4412 (p)
REVERT: R  104 TYR cc_start: 0.4035 (m-80) cc_final: 0.3606 (m-80)
REVERT: R  281 TRP cc_start: 0.4973 (m100) cc_final: 0.4097 (m100)
REVERT: R  333 ARG cc_start: 0.4996 (pmt170) cc_final: 0.3781 (tpp-160)
REVERT: A    9 ASP cc_start: 0.7327 (t70) cc_final: 0.6951 (t0)
REVERT: C   42 GLU cc_start: 0.8229 (pt0) cc_final: 0.7991 (pt0)
REVERT: C   62 ARG cc_start: 0.6804 (mtm-85) cc_final: 0.6567 (mtm110)
  outliers start: 22
  outliers final: 14
  residues processed: 124
  average time/residue: 0.0825
  time to fit residues: 13.7691
Evaluate side-chains
  118 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  220 THR
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  311 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 82 optimal weight:    0.0670
   chunk 62 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 58 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 73 optimal weight:   10.0000
   chunk 18 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 86 optimal weight:    0.0270
   overall best weight:    0.4976

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

Flipped N/Q/H residues before XYZ refinement:
R 285 HIS
A 294 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4720 r_free = 0.4720 target = 0.213066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.171050 restraints weight = 7645.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.4318 rms_B_bonded: 3.12
r_work: 0.3984 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6859
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6944  Z= 0.117
  Angle     :  0.543   6.335   9477  Z= 0.275
  Chirality :  0.041   0.162   1125
  Planarity :  0.003   0.029   1203
  Dihedral  :  3.675  34.009    978
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 19.70 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.28), residues: 907
  helix:  2.10 (0.27), residues: 376
  sheet: -0.38 (0.41), residues: 141
  loop : -1.30 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  15 
 TYR   0.012   0.001   TYR R 213 
 PHE   0.018   0.001   PHE B 199 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.010   0.001   HIS R 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6942)
  covalent geometry    : angle       0.54284 ( 9475)
  SS BOND              : bond        0.00230 (    1)
  SS BOND              : angle       1.41521 (    2)
  hydrogen bonds       : bond        0.02993 (  368)
  hydrogen bonds       : angle       4.15348 ( 1068)
  Misc. bond           : bond        0.00014 (    1)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.269 
Fit side-chains
REVERT: R   49 SER cc_start: 0.5139 (t) cc_final: 0.4447 (p)
REVERT: R  104 TYR cc_start: 0.4148 (m-80) cc_final: 0.3692 (m-80)
REVERT: R  281 TRP cc_start: 0.5038 (m100) cc_final: 0.4167 (m100)
REVERT: R  333 ARG cc_start: 0.4972 (pmt170) cc_final: 0.3769 (tpp-160)
REVERT: A    9 ASP cc_start: 0.7315 (t70) cc_final: 0.6952 (t0)
REVERT: B  105 TYR cc_start: 0.8387 (t80) cc_final: 0.8157 (t80)
REVERT: C   62 ARG cc_start: 0.6767 (mtm-85) cc_final: 0.6539 (mtm110)
  outliers start: 21
  outliers final: 14
  residues processed: 128
  average time/residue: 0.0812
  time to fit residues: 13.9103
Evaluate side-chains
  117 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   82 TYR
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  242 ARG
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0770
   chunk 63 optimal weight:    0.8980
   chunk 22 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 86 optimal weight:    6.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
A 304 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4708 r_free = 0.4708 target = 0.212099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.172020 restraints weight = 7529.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.4301 rms_B_bonded: 3.09
r_work: 0.3960 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6890
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6944  Z= 0.127
  Angle     :  0.548   6.318   9477  Z= 0.279
  Chirality :  0.041   0.143   1125
  Planarity :  0.003   0.029   1203
  Dihedral  :  3.747  36.252    978
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 20.15 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.28), residues: 907
  helix:  2.28 (0.27), residues: 376
  sheet: -0.60 (0.41), residues: 146
  loop : -1.21 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  49 
 TYR   0.011   0.001   TYR R 225 
 PHE   0.018   0.001   PHE R 316 
 TRP   0.009   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6942)
  covalent geometry    : angle       0.54789 ( 9475)
  SS BOND              : bond        0.00207 (    1)
  SS BOND              : angle       1.32953 (    2)
  hydrogen bonds       : bond        0.02866 (  368)
  hydrogen bonds       : angle       4.03269 ( 1068)
  Misc. bond           : bond        0.00016 (    1)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.160 
Fit side-chains
REVERT: R   49 SER cc_start: 0.4971 (t) cc_final: 0.4300 (p)
REVERT: R  104 TYR cc_start: 0.4118 (m-80) cc_final: 0.3652 (m-80)
REVERT: R  210 MET cc_start: 0.4121 (tpp) cc_final: 0.3605 (tpp)
REVERT: R  281 TRP cc_start: 0.5154 (m100) cc_final: 0.4895 (m100)
REVERT: R  333 ARG cc_start: 0.5077 (pmt170) cc_final: 0.3790 (tpp-160)
REVERT: A  247 MET cc_start: 0.7329 (mtm) cc_final: 0.7121 (ptm)
REVERT: B  105 TYR cc_start: 0.8406 (t80) cc_final: 0.8109 (t80)
  outliers start: 28
  outliers final: 22
  residues processed: 127
  average time/residue: 0.0687
  time to fit residues: 11.8105
Evaluate side-chains
  125 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   82 TYR
Chi-restraints excluded: chain R residue  177 PHE
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  311 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0970
   chunk 80 optimal weight:    0.0980
   chunk 79 optimal weight:    0.7980
   chunk 26 optimal weight:    9.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
R 285 HIS
A 294 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4702 r_free = 0.4702 target = 0.211083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.169065 restraints weight = 7597.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.4296 rms_B_bonded: 3.17
r_work: 0.3966 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6886
moved from start:          0.2867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6944  Z= 0.121
  Angle     :  0.546   6.389   9477  Z= 0.278
  Chirality :  0.040   0.144   1125
  Planarity :  0.003   0.029   1203
  Dihedral  :  3.778  36.732    978
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 20.45 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.28), residues: 907
  helix:  2.32 (0.27), residues: 377
  sheet: -0.70 (0.41), residues: 146
  loop : -1.20 (0.29), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  15 
 TYR   0.009   0.001   TYR B  59 
 PHE   0.018   0.001   PHE R 316 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.006   0.001   HIS R 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6942)
  covalent geometry    : angle       0.54621 ( 9475)
  SS BOND              : bond        0.00115 (    1)
  SS BOND              : angle       1.14995 (    2)
  hydrogen bonds       : bond        0.02772 (  368)
  hydrogen bonds       : angle       4.01987 ( 1068)
  Misc. bond           : bond        0.00013 (    1)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 109
  time to evaluate  : 0.293 
Fit side-chains
REVERT: R   49 SER cc_start: 0.5034 (t) cc_final: 0.4350 (p)
REVERT: R  104 TYR cc_start: 0.4069 (m-80) cc_final: 0.3595 (m-80)
REVERT: R  210 MET cc_start: 0.4039 (tpp) cc_final: 0.3552 (tpp)
REVERT: R  281 TRP cc_start: 0.5343 (m100) cc_final: 0.5106 (m100)
REVERT: R  333 ARG cc_start: 0.5069 (pmt170) cc_final: 0.3783 (tpp-160)
REVERT: A  247 MET cc_start: 0.7371 (mtm) cc_final: 0.7155 (ptm)
REVERT: B  105 TYR cc_start: 0.8398 (t80) cc_final: 0.8181 (t80)
REVERT: B  340 ASN cc_start: 0.5898 (OUTLIER) cc_final: 0.5687 (t0)
  outliers start: 32
  outliers final: 22
  residues processed: 128
  average time/residue: 0.0766
  time to fit residues: 13.5468
Evaluate side-chains
  123 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   82 TYR
Chi-restraints excluded: chain R residue  177 PHE
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  242 ARG
Chi-restraints excluded: chain R residue  311 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 49 optimal weight:    0.4980
   chunk 1 optimal weight:    0.8980
   chunk 69 optimal weight:    4.9990
   chunk 58 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 14 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 71 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.208879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.166792 restraints weight = 7477.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.4276 rms_B_bonded: 3.06
r_work: 0.3938 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6944  Z= 0.133
  Angle     :  0.574   9.490   9477  Z= 0.288
  Chirality :  0.041   0.303   1125
  Planarity :  0.003   0.030   1203
  Dihedral  :  3.843  37.797    978
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 21.34 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.28), residues: 907
  helix:  2.33 (0.27), residues: 377
  sheet: -0.74 (0.41), residues: 145
  loop : -1.17 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  15 
 TYR   0.019   0.001   TYR B  59 
 PHE   0.020   0.001   PHE R 316 
 TRP   0.009   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6942)
  covalent geometry    : angle       0.57345 ( 9475)
  SS BOND              : bond        0.00103 (    1)
  SS BOND              : angle       1.45210 (    2)
  hydrogen bonds       : bond        0.02806 (  368)
  hydrogen bonds       : angle       4.01642 ( 1068)
  Misc. bond           : bond        0.00016 (    1)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 107
  time to evaluate  : 0.253 
Fit side-chains
REVERT: R   49 SER cc_start: 0.5207 (t) cc_final: 0.4547 (p)
REVERT: R  104 TYR cc_start: 0.4043 (m-80) cc_final: 0.3554 (m-80)
REVERT: R  210 MET cc_start: 0.4076 (tpp) cc_final: 0.3675 (tpp)
REVERT: R  281 TRP cc_start: 0.5489 (m100) cc_final: 0.5249 (m100)
REVERT: R  333 ARG cc_start: 0.4928 (pmt170) cc_final: 0.3749 (tmt170)
REVERT: A  247 MET cc_start: 0.7349 (mtm) cc_final: 0.7025 (ptm)
REVERT: B  105 TYR cc_start: 0.8428 (t80) cc_final: 0.8199 (t80)
  outliers start: 30
  outliers final: 22
  residues processed: 125
  average time/residue: 0.0752
  time to fit residues: 12.9216
Evaluate side-chains
  122 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  177 PHE
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  242 ARG
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  311 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  294 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9980
   chunk 87 optimal weight:    5.9990
   chunk 37 optimal weight:    0.2980
   chunk 44 optimal weight:    0.0010
   chunk 69 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 60 optimal weight:    0.3980
   chunk 31 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
R 285 HIS
A 294 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.210065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.166904 restraints weight = 7598.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.4278 rms_B_bonded: 3.29
r_work: 0.3932 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6956
moved from start:          0.3128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6944  Z= 0.120
  Angle     :  0.567   9.460   9477  Z= 0.285
  Chirality :  0.041   0.288   1125
  Planarity :  0.003   0.030   1203
  Dihedral  :  3.784  37.348    978
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 22.24 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.28), residues: 907
  helix:  2.34 (0.26), residues: 377
  sheet: -0.75 (0.42), residues: 145
  loop : -1.14 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  15 
 TYR   0.017   0.001   TYR B  59 
 PHE   0.032   0.001   PHE R 316 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.006   0.001   HIS R 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6942)
  covalent geometry    : angle       0.56656 ( 9475)
  SS BOND              : bond        0.00159 (    1)
  SS BOND              : angle       1.54518 (    2)
  hydrogen bonds       : bond        0.02703 (  368)
  hydrogen bonds       : angle       3.95403 ( 1068)
  Misc. bond           : bond        0.00010 (    1)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 0.267 
Fit side-chains
REVERT: R   49 SER cc_start: 0.4999 (t) cc_final: 0.4332 (p)
REVERT: R  169 ILE cc_start: 0.4484 (OUTLIER) cc_final: 0.4158 (tp)
REVERT: R  210 MET cc_start: 0.4042 (tpp) cc_final: 0.3676 (tpp)
REVERT: R  281 TRP cc_start: 0.5538 (m100) cc_final: 0.4635 (m100)
REVERT: R  333 ARG cc_start: 0.5151 (pmt170) cc_final: 0.3856 (tmt170)
REVERT: A  247 MET cc_start: 0.7471 (mtm) cc_final: 0.7251 (ptp)
  outliers start: 30
  outliers final: 21
  residues processed: 123
  average time/residue: 0.0702
  time to fit residues: 11.9073
Evaluate side-chains
  120 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  242 ARG
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  311 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  294 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 53 optimal weight:   20.0000
   chunk 21 optimal weight:    5.9990
   chunk 46 optimal weight:    8.9990
   chunk 9 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 48 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** R 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.205364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.148054 restraints weight = 7622.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.4044 rms_B_bonded: 2.59
r_work: 0.3898 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.3399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6944  Z= 0.169
  Angle     :  0.617   9.538   9477  Z= 0.309
  Chirality :  0.042   0.281   1125
  Planarity :  0.003   0.033   1203
  Dihedral  :  4.036  39.108    978
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 22.54 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.28), residues: 907
  helix:  2.22 (0.26), residues: 378
  sheet: -0.89 (0.39), residues: 155
  loop : -1.18 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  15 
 TYR   0.012   0.002   TYR A 287 
 PHE   0.031   0.001   PHE R 316 
 TRP   0.012   0.001   TRP B  99 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 6942)
  covalent geometry    : angle       0.61696 ( 9475)
  SS BOND              : bond        0.00161 (    1)
  SS BOND              : angle       1.59735 (    2)
  hydrogen bonds       : bond        0.02946 (  368)
  hydrogen bonds       : angle       4.08473 ( 1068)
  Misc. bond           : bond        0.00022 (    1)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 110
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: R   49 SER cc_start: 0.5065 (t) cc_final: 0.4419 (p)
REVERT: R  169 ILE cc_start: 0.4566 (OUTLIER) cc_final: 0.4264 (tp)
REVERT: R  263 ARG cc_start: 0.4944 (tmm160) cc_final: 0.4302 (tmm160)
REVERT: R  333 ARG cc_start: 0.5024 (pmt170) cc_final: 0.3737 (tmt170)
REVERT: A  247 MET cc_start: 0.7526 (mtm) cc_final: 0.7283 (ptm)
  outliers start: 28
  outliers final: 22
  residues processed: 126
  average time/residue: 0.0711
  time to fit residues: 12.5292
Evaluate side-chains
  126 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  177 PHE
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  242 ARG
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  311 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  294 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 80 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0670
   chunk 29 optimal weight:    3.9990
   chunk 86 optimal weight:    8.9990
   chunk 4 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0970
   chunk 9 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
** R 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4674 r_free = 0.4674 target = 0.208287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.164250 restraints weight = 7571.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.4236 rms_B_bonded: 3.37
r_work: 0.3891 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6934
moved from start:          0.3397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6944  Z= 0.127
  Angle     :  0.606   9.548   9477  Z= 0.300
  Chirality :  0.041   0.279   1125
  Planarity :  0.003   0.035   1203
  Dihedral  :  3.913  39.031    978
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 23.88 %
    Favored  : 72.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.28), residues: 907
  helix:  2.31 (0.26), residues: 377
  sheet: -0.71 (0.40), residues: 159
  loop : -1.17 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  15 
 TYR   0.012   0.001   TYR A 287 
 PHE   0.029   0.001   PHE R 316 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6942)
  covalent geometry    : angle       0.60562 ( 9475)
  SS BOND              : bond        0.00092 (    1)
  SS BOND              : angle       1.43088 (    2)
  hydrogen bonds       : bond        0.02829 (  368)
  hydrogen bonds       : angle       4.00958 ( 1068)
  Misc. bond           : bond        0.00010 (    1)

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: R   49 SER cc_start: 0.5069 (t) cc_final: 0.4427 (p)
REVERT: R  169 ILE cc_start: 0.4525 (OUTLIER) cc_final: 0.4225 (tp)
REVERT: R  210 MET cc_start: 0.3907 (tpp) cc_final: 0.3452 (tpp)
REVERT: R  333 ARG cc_start: 0.5033 (pmt170) cc_final: 0.3698 (tmt170)
REVERT: A  247 MET cc_start: 0.7547 (mtm) cc_final: 0.7268 (ptm)
  outliers start: 24
  outliers final: 22
  residues processed: 118
  average time/residue: 0.0700
  time to fit residues: 11.5546
Evaluate side-chains
  125 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  177 PHE
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  242 ARG
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  311 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  294 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 75 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 83 optimal weight:    0.4980
   chunk 74 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9980
   chunk 29 optimal weight:    0.3980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** R 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.207931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.165634 restraints weight = 7660.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.4263 rms_B_bonded: 3.30
r_work: 0.3907 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6944  Z= 0.135
  Angle     :  0.604   9.038   9477  Z= 0.300
  Chirality :  0.042   0.279   1125
  Planarity :  0.003   0.034   1203
  Dihedral  :  3.918  38.569    978
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 24.33 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.28), residues: 907
  helix:  2.30 (0.26), residues: 378
  sheet: -0.67 (0.41), residues: 154
  loop : -1.20 (0.30), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  15 
 TYR   0.011   0.001   TYR A 287 
 PHE   0.031   0.001   PHE R 316 
 TRP   0.020   0.001   TRP B  99 
 HIS   0.004   0.001   HIS R 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6942)
  covalent geometry    : angle       0.60353 ( 9475)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       1.38588 (    2)
  hydrogen bonds       : bond        0.02792 (  368)
  hydrogen bonds       : angle       3.98366 ( 1068)
  Misc. bond           : bond        0.00013 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2071.13 seconds
wall clock time: 36 minutes 9.73 seconds (2169.73 seconds total)