Starting phenix.real_space_refine
on Tue Feb  3 18:10:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9o6k_70174/02_2026/9o6k_70174_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9o6k_70174/02_2026/9o6k_70174.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9o6k_70174/02_2026/9o6k_70174_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9o6k_70174/02_2026/9o6k_70174_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9o6k_70174/02_2026/9o6k_70174.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9o6k_70174/02_2026/9o6k_70174.map"
  }
  resolution = 3.59
  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=   0.025
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      25      5.16       5
     C    3693      2.51       5
     N    1029      2.21       5
     O    1100      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5847
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1937
          Classifications: {'peptide': 254}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 7, 'TRANS': 246}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 164
          Unresolved non-hydrogen angles: 205
          Unresolved non-hydrogen dihedrals: 146
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2, 'TRP:plan': 2, 'GLN:plan1': 3, 'PHE:plan': 3, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 85
    Chain: "B"
      Number of atoms: 1798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1798
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 8, 'TRANS': 226}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 126
          Unresolved non-hydrogen angles: 155
          Unresolved non-hydrogen dihedrals: 110
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 5, 'GLN:plan1': 2, 'PHE:plan': 2, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 82
    Chain: "C"
      Number of atoms: 1152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1152
          Classifications: {'peptide': 144}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 3, 'TRANS': 140}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "H"
      Number of atoms: 934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 934
          Classifications: {'peptide': 122}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 1, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 3, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "B"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Classifications: {'peptide': 1}
  Time building chain proxies: 1.16, per 1000 atoms: 0.20
  Number of scatterers: 5847
  At special positions: 0
  Unit cell: (74.624, 103.117, 119.398, 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      25     16.00
     O    1100      8.00
     N    1029      7.00
     C    3693      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 338.9 milliseconds
  

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1426

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 3 sheets defined
      43.2% alpha, 9.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 101 through 106
      removed outlier: 3.518A  pdb=" N   LEU A 105 " --> pdb=" O   GLN A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 111
    Processing helix  chain 'A' and resid 138 through 142
    Processing helix  chain 'A' and resid 166 through 171
      removed outlier: 3.940A  pdb=" N   LEU A 170 " --> pdb=" O   ASN A 166 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   SER A 171 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 166 through 171'
    Processing helix  chain 'A' and resid 190 through 194
    Processing helix  chain 'A' and resid 201 through 205
    Processing helix  chain 'A' and resid 218 through 228
    Processing helix  chain 'A' and resid 321 through 335
      removed outlier: 4.412A  pdb=" N   GLU A 328 " --> pdb=" O   GLN A 324 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   LYS A 329 " --> pdb=" O   VAL A 325 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LYS A 330 " --> pdb=" O   THR A 326 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ASN A 335 " --> pdb=" O   PHE A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 342
      removed outlier: 4.029A  pdb=" N   SER A 341 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 348
      removed outlier: 3.711A  pdb=" N   PHE A 348 " --> pdb=" O   ASN A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 415
    Processing helix  chain 'B' and resid 136 through 165
      removed outlier: 4.265A  pdb=" N   LEU B 142 " --> pdb=" O   GLY B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 199
      removed outlier: 3.717A  pdb=" N   LEU B 191 " --> pdb=" O   ASN B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 238
      removed outlier: 3.889A  pdb=" N   MET B 238 " --> pdb=" O   LYS B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 244
    Processing helix  chain 'B' and resid 254 through 256
      No H-bonds generated for 'chain 'B' and resid 254 through 256'
    Processing helix  chain 'B' and resid 257 through 267
    Processing helix  chain 'B' and resid 336 through 346
      removed outlier: 3.705A  pdb=" N   GLN B 340 " --> pdb=" O   GLU B 336 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 40
    Processing helix  chain 'C' and resid 44 through 52
    Processing helix  chain 'C' and resid 58 through 71
      removed outlier: 3.526A  pdb=" N   GLY C  71 " --> pdb=" O   GLN C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 75 through 79
      removed outlier: 3.895A  pdb=" N   MET C  79 " --> pdb=" O   GLY C  76 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 84 through 95
    Processing helix  chain 'C' and resid 100 through 104
    Processing helix  chain 'C' and resid 113 through 128
    Processing helix  chain 'C' and resid 162 through 184
      removed outlier: 4.060A  pdb=" N   ASN C 172 " --> pdb=" O   THR C 168 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 13 through 26
    Processing helix  chain 'H' and resid 38 through 44
      removed outlier: 3.836A  pdb=" N   PHE H  42 " --> pdb=" O   ASN H  38 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 51 through 66
      removed outlier: 3.673A  pdb=" N   PHE H  65 " --> pdb=" O   GLY H  61 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 91
    Processing helix  chain 'H' and resid 100 through 104
      removed outlier: 3.555A  pdb=" N   TYR H 104 " --> pdb=" O   THR H 101 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 113 through 119
      removed outlier: 3.946A  pdb=" N   SER H 119 " --> pdb=" O   GLU H 115 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 125 through 129
      removed outlier: 3.671A  pdb=" N   ASN H 128 " --> pdb=" O   LYS H 125 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 128
      removed outlier: 6.470A  pdb=" N   LYS A 126 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   TRP A 188 " --> pdb=" O   ILE A 150 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   THR A 362 " --> pdb=" O   SER A 189 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   MET A 365 " --> pdb=" O   GLU A 210 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   GLU A 210 " --> pdb=" O   MET A 365 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ARG A 367 " --> pdb=" O   TYR A 208 " (cutoff:3.500A)
      removed outlier: 5.513A  pdb=" N   TYR A 208 " --> pdb=" O   ARG A 367 " (cutoff:3.500A)
      removed outlier: 8.122A  pdb=" N   GLU A 389 " --> pdb=" O   SER A 213 " (cutoff:3.500A)
      removed outlier: 5.456A  pdb=" N   MET A 215 " --> pdb=" O   GLU A 389 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 176 through 179
    Processing sheet with id=AA3, first strand: chain 'B' and resid 323 through 327
      removed outlier: 3.857A  pdb=" N   ASP B 274 " --> pdb=" O   ILE B 304 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER B 301 " --> pdb=" O   ALA B 253 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE B 249 " --> pdb=" O   GLY B 305 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LYS B 307 " --> pdb=" O   GLY B 247 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   GLY B 247 " --> pdb=" O   LYS B 307 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ILE B 206 " --> pdb=" O   PHE B 250 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   TRP B 252 " --> pdb=" O   ILE B 206 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   MET B 208 " --> pdb=" O   TRP B 252 " (cutoff:3.500A)

    223 hydrogen bonds defined for protein.
    618 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: 0.68 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1954
        1.34 -     1.46: 853
        1.46 -     1.57: 3090
        1.57 -     1.69: 0
        1.69 -     1.81: 41
  Bond restraints: 5938
  Sorted by residual:
  bond pdb=" N   ILE A 133 "
       pdb=" CA  ILE A 133 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.040 1.25e-02 6.40e+03 1.01e+01
  bond pdb=" N   ASN A 132 "
       pdb=" CA  ASN A 132 "
    ideal  model  delta    sigma   weight residual
    1.454  1.492 -0.038 1.23e-02 6.61e+03 9.50e+00
  bond pdb=" N   ASP B 228 "
       pdb=" CA  ASP B 228 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.034 1.22e-02 6.72e+03 7.81e+00
  bond pdb=" N   TYR H  49 "
       pdb=" CA  TYR H  49 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.29e-02 6.01e+03 7.81e+00
  bond pdb=" N   LEU B 230 "
       pdb=" CA  LEU B 230 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.25e-02 6.40e+03 7.02e+00
  ... (remaining 5933 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 7679
        1.58 -     3.15: 273
        3.15 -     4.73: 42
        4.73 -     6.30: 16
        6.30 -     7.88: 4
  Bond angle restraints: 8014
  Sorted by residual:
  angle pdb=" N   PHE A 134 "
        pdb=" CA  PHE A 134 "
        pdb=" C   PHE A 134 "
      ideal   model   delta    sigma   weight residual
     113.19  108.14    5.05 1.19e+00 7.06e-01 1.80e+01
  angle pdb=" N   LEU B 230 "
        pdb=" CA  LEU B 230 "
        pdb=" C   LEU B 230 "
      ideal   model   delta    sigma   weight residual
     112.93  108.46    4.47 1.12e+00 7.97e-01 1.60e+01
  angle pdb=" N   LYS A 135 "
        pdb=" CA  LYS A 135 "
        pdb=" C   LYS A 135 "
      ideal   model   delta    sigma   weight residual
     114.04  109.57    4.47 1.24e+00 6.50e-01 1.30e+01
  angle pdb=" CA  ILE B 150 "
        pdb=" C   ILE B 150 "
        pdb=" O   ILE B 150 "
      ideal   model   delta    sigma   weight residual
     121.41  117.88    3.53 1.04e+00 9.25e-01 1.15e+01
  angle pdb=" C   ASP A 137 "
        pdb=" N   LEU A 138 "
        pdb=" CA  LEU A 138 "
      ideal   model   delta    sigma   weight residual
     122.26  117.17    5.09 1.59e+00 3.96e-01 1.03e+01
  ... (remaining 8009 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 3273
       17.98 -    35.96: 272
       35.96 -    53.94: 39
       53.94 -    71.92: 10
       71.92 -    89.90: 9
  Dihedral angle restraints: 3603
    sinusoidal: 1409
      harmonic: 2194
  Sorted by residual:
  dihedral pdb=" CA  TRP B 365 "
           pdb=" C   TRP B 365 "
           pdb=" N   VAL B 366 "
           pdb=" CA  VAL B 366 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.30   22.70     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" CA  MET B 202 "
           pdb=" C   MET B 202 "
           pdb=" N   PHE B 203 "
           pdb=" CA  PHE B 203 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.11  -18.89     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  MET A 403 "
           pdb=" C   MET A 403 "
           pdb=" N   LYS A 404 "
           pdb=" CA  LYS A 404 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.49   18.51     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 3600 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 543
       0.032 -    0.063: 231
       0.063 -    0.094: 75
       0.094 -    0.126: 40
       0.126 -    0.157: 11
  Chirality restraints: 900
  Sorted by residual:
  chirality pdb=" CA  ILE A 214 "
            pdb=" N   ILE A 214 "
            pdb=" C   ILE A 214 "
            pdb=" CB  ILE A 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.19e-01
  chirality pdb=" CB  ILE A 369 "
            pdb=" CA  ILE A 369 "
            pdb=" CG1 ILE A 369 "
            pdb=" CG2 ILE A 369 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.94e-01
  chirality pdb=" CA  ILE A 133 "
            pdb=" N   ILE A 133 "
            pdb=" C   ILE A 133 "
            pdb=" CB  ILE A 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.87e-01
  ... (remaining 897 not shown)

  Planarity restraints: 1038
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 130 "    0.020 2.00e-02 2.50e+03   4.00e-02 1.60e+01
        pdb=" C   VAL A 130 "   -0.069 2.00e-02 2.50e+03
        pdb=" O   VAL A 130 "    0.026 2.00e-02 2.50e+03
        pdb=" N   LYS A 131 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  70 "   -0.016 2.00e-02 2.50e+03   1.39e-02 4.80e+00
        pdb=" CG  TRP H  70 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  70 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  70 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  70 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  70 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  70 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  70 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  70 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  70 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 145 "    0.009 2.00e-02 2.50e+03   1.84e-02 3.40e+00
        pdb=" C   ASP B 145 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   ASP B 145 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ILE B 146 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1035 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1636
        2.81 -     3.34: 6072
        3.34 -     3.86: 9498
        3.86 -     4.38: 11107
        4.38 -     4.90: 17730
  Nonbonded interactions: 46043
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 355 "
            pdb=" N   SAH B 401 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" O   SER B 231 "
            pdb=" N   LYS B 234 "
     model   vdw
     2.435 3.120
  nonbonded pdb=" OG  SER H  40 "
            pdb=" OH  TYR H  49 "
     model   vdw
     2.468 3.040
  nonbonded pdb=" O   ASN B 162 "
            pdb=" ND2 ASN B 162 "
     model   vdw
     2.517 3.120
  nonbonded pdb=" O   HIS C 169 "
            pdb=" OD1 ASN C 172 "
     model   vdw
     2.550 3.040
  ... (remaining 46038 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.900
  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:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.240
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6232
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5938  Z= 0.202
  Angle     :  0.712   7.880   8014  Z= 0.398
  Chirality :  0.045   0.157    900
  Planarity :  0.004   0.061   1038
  Dihedral  : 14.188  89.901   2177
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  0.34 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.31), residues: 737
  helix: -0.15 (0.32), residues: 251
  sheet: -1.62 (0.52), residues: 89
  loop : -1.31 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  90 
 TYR   0.023   0.002   TYR B 294 
 PHE   0.021   0.002   PHE C  89 
 TRP   0.037   0.002   TRP H  70 
 HIS   0.002   0.001   HIS B 152 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 5938)
  covalent geometry    : angle       0.71186 ( 8014)
  hydrogen bonds       : bond        0.15776 (  223)
  hydrogen bonds       : angle       7.92011 (  618)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 123
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 PHE cc_start: 0.9269 (t80) cc_final: 0.9031 (t80)
REVERT: A  404 LYS cc_start: 0.8510 (tttt) cc_final: 0.8267 (tptt)
REVERT: B  176 SER cc_start: 0.8743 (t) cc_final: 0.7987 (p)
REVERT: B  262 ILE cc_start: 0.6635 (mt) cc_final: 0.6326 (mp)
REVERT: B  266 GLU cc_start: 0.8009 (tp30) cc_final: 0.7021 (mp0)
REVERT: B  294 TYR cc_start: 0.5454 (m-10) cc_final: 0.4364 (m-10)
REVERT: H   21 MET cc_start: 0.8787 (mtp) cc_final: 0.8488 (mtp)
REVERT: H   38 ASN cc_start: 0.6647 (t0) cc_final: 0.6237 (t0)
REVERT: H  104 TYR cc_start: 0.8521 (m-10) cc_final: 0.8280 (m-10)
  outliers start: 2
  outliers final: 1
  residues processed: 124
  average time/residue: 0.0948
  time to fit residues: 14.8376
Evaluate side-chains
  90 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    0.1980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.4980
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
A 224 GLN
B 162 ASN
B 195 GLN
B 198 HIS
B 255 ASN
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
H  55 GLN
H  98 ASN
H 120 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4805 r_free = 0.4805 target = 0.159454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.117813 restraints weight = 14343.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.121787 restraints weight = 8663.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.124738 restraints weight = 6119.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.126886 restraints weight = 4738.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.128453 restraints weight = 3948.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6305
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5938  Z= 0.156
  Angle     :  0.655   9.664   8014  Z= 0.338
  Chirality :  0.043   0.145    900
  Planarity :  0.004   0.042   1038
  Dihedral  :  4.988  38.565    800
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  8.91 %
    Favored  : 89.92 %
  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: -0.98 (0.31), residues: 737
  helix:  0.44 (0.32), residues: 256
  sheet: -1.47 (0.53), residues: 91
  loop : -1.17 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 379 
 TYR   0.017   0.002   TYR B 270 
 PHE   0.016   0.002   PHE B 293 
 TRP   0.021   0.002   TRP H  50 
 HIS   0.003   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 5938)
  covalent geometry    : angle       0.65456 ( 8014)
  hydrogen bonds       : bond        0.03935 (  223)
  hydrogen bonds       : angle       5.87149 (  618)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.7830 (mmp) cc_final: 0.6652 (tpt)
REVERT: A  331 PHE cc_start: 0.9184 (t80) cc_final: 0.8877 (t80)
REVERT: A  333 MET cc_start: 0.5420 (tpp) cc_final: 0.4498 (tpt)
REVERT: B  293 PHE cc_start: 0.6597 (t80) cc_final: 0.6306 (t80)
REVERT: B  294 TYR cc_start: 0.5419 (m-10) cc_final: 0.4733 (m-10)
REVERT: H   21 MET cc_start: 0.8949 (mtp) cc_final: 0.8501 (mtp)
REVERT: H   38 ASN cc_start: 0.6595 (t0) cc_final: 0.6180 (t0)
REVERT: H  104 TYR cc_start: 0.8468 (m-10) cc_final: 0.8216 (m-10)
  outliers start: 7
  outliers final: 6
  residues processed: 98
  average time/residue: 0.0884
  time to fit residues: 11.1959
Evaluate side-chains
  94 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  134 PHE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain C residue  157 GLU
Chi-restraints excluded: chain H residue   32 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 30 optimal weight:    0.3980
   chunk 1 optimal weight:    0.2980
   chunk 47 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 73 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
B 267 ASN
B 359 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4808 r_free = 0.4808 target = 0.158792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.118019 restraints weight = 14264.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.122031 restraints weight = 8416.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.124804 restraints weight = 6000.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.126742 restraints weight = 4688.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.128232 restraints weight = 3924.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.4335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6307
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5938  Z= 0.122
  Angle     :  0.603   9.107   8014  Z= 0.311
  Chirality :  0.043   0.231    900
  Planarity :  0.003   0.027   1038
  Dihedral  :  4.705  30.980    800
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 10.92 %
    Favored  : 88.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.31), residues: 737
  helix:  0.72 (0.32), residues: 257
  sheet: -1.34 (0.55), residues: 90
  loop : -1.04 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 259 
 TYR   0.016   0.002   TYR H  17 
 PHE   0.024   0.002   PHE B 355 
 TRP   0.018   0.001   TRP H  50 
 HIS   0.003   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 5938)
  covalent geometry    : angle       0.60309 ( 8014)
  hydrogen bonds       : bond        0.03392 (  223)
  hydrogen bonds       : angle       5.54575 (  618)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.7682 (mmp) cc_final: 0.6836 (tpt)
REVERT: A  331 PHE cc_start: 0.9145 (t80) cc_final: 0.8864 (t80)
REVERT: A  333 MET cc_start: 0.5056 (tpp) cc_final: 0.4164 (tpt)
REVERT: B  293 PHE cc_start: 0.6699 (t80) cc_final: 0.6340 (t80)
REVERT: B  294 TYR cc_start: 0.5394 (m-10) cc_final: 0.4590 (m-10)
REVERT: H   21 MET cc_start: 0.8926 (mtp) cc_final: 0.8374 (mtm)
REVERT: H   38 ASN cc_start: 0.6683 (t0) cc_final: 0.6260 (t0)
REVERT: H  104 TYR cc_start: 0.8422 (m-10) cc_final: 0.8161 (m-10)
  outliers start: 5
  outliers final: 4
  residues processed: 96
  average time/residue: 0.0811
  time to fit residues: 10.1896
Evaluate side-chains
  92 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain H residue   17 TYR
Chi-restraints excluded: chain H residue   32 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0000
   chunk 4 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 54 optimal weight:    0.1980
   chunk 52 optimal weight:    0.9980
   chunk 61 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0370
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.3862

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

Flipped N/Q/H residues before XYZ refinement:
B 359 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4839 r_free = 0.4839 target = 0.161227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.120445 restraints weight = 14346.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.124588 restraints weight = 8563.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.127531 restraints weight = 5951.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.129717 restraints weight = 4588.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.131250 restraints weight = 3784.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.4420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6187
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5938  Z= 0.099
  Angle     :  0.556  10.660   8014  Z= 0.287
  Chirality :  0.041   0.202    900
  Planarity :  0.003   0.029   1038
  Dihedral  :  4.158  20.366    798
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.60 %
    Favored  : 86.89 %
  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: -0.42 (0.32), residues: 737
  helix:  0.96 (0.33), residues: 258
  sheet: -0.94 (0.55), residues: 89
  loop : -0.95 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 259 
 TYR   0.015   0.001   TYR H  17 
 PHE   0.018   0.001   PHE B 355 
 TRP   0.012   0.001   TRP H  50 
 HIS   0.002   0.000   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 5938)
  covalent geometry    : angle       0.55609 ( 8014)
  hydrogen bonds       : bond        0.02899 (  223)
  hydrogen bonds       : angle       5.19407 (  618)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 PHE cc_start: 0.9130 (t80) cc_final: 0.8884 (t80)
REVERT: A  379 ARG cc_start: 0.8130 (ttt90) cc_final: 0.7727 (ttp-170)
REVERT: B  293 PHE cc_start: 0.6858 (t80) cc_final: 0.6414 (t80)
REVERT: B  294 TYR cc_start: 0.5398 (m-10) cc_final: 0.4556 (m-10)
REVERT: H   21 MET cc_start: 0.8861 (mtp) cc_final: 0.8239 (mtp)
REVERT: H   38 ASN cc_start: 0.6426 (t0) cc_final: 0.5951 (t0)
REVERT: H  104 TYR cc_start: 0.8467 (m-10) cc_final: 0.8248 (m-10)
  outliers start: 9
  outliers final: 6
  residues processed: 96
  average time/residue: 0.0886
  time to fit residues: 11.0141
Evaluate side-chains
  90 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain H residue   17 TYR
Chi-restraints excluded: chain H residue   32 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 1 optimal weight:    0.0870
   chunk 14 optimal weight:    0.0040
   chunk 64 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 70 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.9572

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

Flipped N/Q/H residues before XYZ refinement:
B 359 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4807 r_free = 0.4807 target = 0.158621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.117593 restraints weight = 14559.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.121636 restraints weight = 8628.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.124502 restraints weight = 6003.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.126544 restraints weight = 4653.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.128069 restraints weight = 3867.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.4371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6261
moved from start:          0.2666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5938  Z= 0.122
  Angle     :  0.561   7.903   8014  Z= 0.295
  Chirality :  0.042   0.234    900
  Planarity :  0.003   0.034   1038
  Dihedral  :  4.217  18.979    798
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 12.27 %
    Favored  : 85.55 %
  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: -0.38 (0.32), residues: 737
  helix:  1.01 (0.33), residues: 258
  sheet: -0.93 (0.55), residues: 90
  loop : -0.93 (0.33), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 149 
 TYR   0.032   0.002   TYR B 153 
 PHE   0.013   0.001   PHE B 355 
 TRP   0.012   0.001   TRP B 252 
 HIS   0.002   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 5938)
  covalent geometry    : angle       0.56070 ( 8014)
  hydrogen bonds       : bond        0.02976 (  223)
  hydrogen bonds       : angle       5.17694 (  618)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 PHE cc_start: 0.9132 (t80) cc_final: 0.8908 (t80)
REVERT: A  379 ARG cc_start: 0.8169 (ttt90) cc_final: 0.7773 (ttp-170)
REVERT: A  402 MET cc_start: 0.7411 (mtm) cc_final: 0.6957 (ptp)
REVERT: B  293 PHE cc_start: 0.6879 (t80) cc_final: 0.6514 (t80)
REVERT: B  294 TYR cc_start: 0.5206 (m-10) cc_final: 0.4446 (m-10)
REVERT: H   21 MET cc_start: 0.9004 (mtp) cc_final: 0.8341 (mtm)
REVERT: H   38 ASN cc_start: 0.6489 (t0) cc_final: 0.6042 (t0)
REVERT: H  104 TYR cc_start: 0.8488 (m-10) cc_final: 0.8284 (m-10)
  outliers start: 13
  outliers final: 10
  residues processed: 95
  average time/residue: 0.0777
  time to fit residues: 9.7523
Evaluate side-chains
  95 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ASN
Chi-restraints excluded: chain A residue  134 PHE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain H residue   17 TYR
Chi-restraints excluded: chain H residue   32 LEU
Chi-restraints excluded: chain H residue   58 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 57 optimal weight:   30.0000
   chunk 54 optimal weight:    0.3980
   chunk 44 optimal weight:    0.0070
   chunk 16 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   overall best weight:    1.4804

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

Flipped N/Q/H residues before XYZ refinement:
** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4774 r_free = 0.4774 target = 0.156935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.115163 restraints weight = 14249.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.119040 restraints weight = 8582.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.121888 restraints weight = 6080.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.123977 restraints weight = 4745.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.125499 restraints weight = 3947.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.4323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6335
moved from start:          0.3032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5938  Z= 0.155
  Angle     :  0.612  11.673   8014  Z= 0.322
  Chirality :  0.042   0.171    900
  Planarity :  0.003   0.032   1038
  Dihedral  :  4.529  18.282    798
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 13.11 %
    Favored  : 84.54 %
  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: -0.44 (0.32), residues: 737
  helix:  0.97 (0.33), residues: 256
  sheet: -1.15 (0.55), residues: 88
  loop : -0.92 (0.34), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 350 
 TYR   0.016   0.002   TYR H  17 
 PHE   0.019   0.002   PHE A 366 
 TRP   0.014   0.002   TRP H  50 
 HIS   0.003   0.001   HIS A 380 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 5938)
  covalent geometry    : angle       0.61232 ( 8014)
  hydrogen bonds       : bond        0.03268 (  223)
  hydrogen bonds       : angle       5.36454 (  618)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 PHE cc_start: 0.9137 (t80) cc_final: 0.8904 (t80)
REVERT: A  350 ARG cc_start: 0.7492 (ptt-90) cc_final: 0.7246 (mtm-85)
REVERT: A  379 ARG cc_start: 0.8224 (ttt90) cc_final: 0.7372 (ttt90)
REVERT: A  382 ARG cc_start: 0.6550 (tpt90) cc_final: 0.4638 (tpt90)
REVERT: A  431 MET cc_start: 0.8040 (pmm) cc_final: 0.7262 (pmm)
REVERT: B  196 MET cc_start: 0.8806 (mmm) cc_final: 0.8477 (mmp)
REVERT: B  294 TYR cc_start: 0.4824 (m-10) cc_final: 0.4355 (m-10)
REVERT: H   21 MET cc_start: 0.9040 (mtp) cc_final: 0.8435 (mtm)
REVERT: H   38 ASN cc_start: 0.6642 (t0) cc_final: 0.6218 (t0)
REVERT: H  104 TYR cc_start: 0.8410 (m-10) cc_final: 0.8165 (m-10)
  outliers start: 14
  outliers final: 10
  residues processed: 95
  average time/residue: 0.0854
  time to fit residues: 10.6158
Evaluate side-chains
  97 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 PHE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue  157 GLU
Chi-restraints excluded: chain H residue   17 TYR
Chi-restraints excluded: chain H residue   32 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 64 optimal weight:    8.9990
   chunk 8 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 44 optimal weight:    0.0670
   chunk 26 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    1.3122

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

Flipped N/Q/H residues before XYZ refinement:
** B 255 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 = 0.4776 r_free = 0.4776 target = 0.155879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.114862 restraints weight = 14476.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.118710 restraints weight = 8737.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.121511 restraints weight = 6197.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.123456 restraints weight = 4824.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.125008 restraints weight = 4026.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.4329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6337
moved from start:          0.3105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5938  Z= 0.147
  Angle     :  0.612  10.188   8014  Z= 0.323
  Chirality :  0.043   0.188    900
  Planarity :  0.003   0.035   1038
  Dihedral  :  4.505  18.516    798
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.96 %
    Favored  : 82.86 %
  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: -0.52 (0.32), residues: 737
  helix:  0.86 (0.33), residues: 260
  sheet: -1.20 (0.54), residues: 87
  loop : -0.96 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 360 
 TYR   0.047   0.002   TYR B 153 
 PHE   0.032   0.002   PHE B 355 
 TRP   0.014   0.001   TRP B 252 
 HIS   0.002   0.001   HIS A 380 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 5938)
  covalent geometry    : angle       0.61215 ( 8014)
  hydrogen bonds       : bond        0.03230 (  223)
  hydrogen bonds       : angle       5.41556 (  618)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 PHE cc_start: 0.9120 (t80) cc_final: 0.8894 (t80)
REVERT: A  350 ARG cc_start: 0.7587 (ptt-90) cc_final: 0.7331 (mtm-85)
REVERT: A  379 ARG cc_start: 0.8220 (ttt90) cc_final: 0.7569 (ttt90)
REVERT: A  382 ARG cc_start: 0.6562 (tpt90) cc_final: 0.4646 (tpt90)
REVERT: A  402 MET cc_start: 0.7514 (mtm) cc_final: 0.6960 (ptp)
REVERT: B  196 MET cc_start: 0.8757 (mmm) cc_final: 0.8352 (mmp)
REVERT: H   21 MET cc_start: 0.8963 (mtp) cc_final: 0.8387 (mtm)
REVERT: H   38 ASN cc_start: 0.6682 (t0) cc_final: 0.6281 (t0)
REVERT: H  104 TYR cc_start: 0.8470 (m-10) cc_final: 0.8224 (m-10)
  outliers start: 13
  outliers final: 9
  residues processed: 93
  average time/residue: 0.0871
  time to fit residues: 10.5742
Evaluate side-chains
  93 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 PHE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain H residue   17 TYR
Chi-restraints excluded: chain H residue   32 LEU
Chi-restraints excluded: chain H residue   58 LEU
Chi-restraints excluded: chain H residue  116 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 73 optimal weight:    0.0020
   chunk 1 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 54 optimal weight:    9.9990
   chunk 66 optimal weight:    0.4980
   chunk 17 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 51 optimal weight:   20.0000
   chunk 59 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.5988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4817 r_free = 0.4817 target = 0.159941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.118530 restraints weight = 14235.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.122709 restraints weight = 8435.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.125729 restraints weight = 5926.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.127878 restraints weight = 4574.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.129516 restraints weight = 3788.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.4379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6265
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5938  Z= 0.117
  Angle     :  0.618  10.542   8014  Z= 0.327
  Chirality :  0.043   0.251    900
  Planarity :  0.003   0.036   1038
  Dihedral  :  4.340  18.777    798
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.11 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.96 %
    Favored  : 83.03 %
  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: -0.42 (0.32), residues: 737
  helix:  0.93 (0.33), residues: 260
  sheet: -1.12 (0.53), residues: 90
  loop : -0.88 (0.34), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 149 
 TYR   0.015   0.001   TYR H  17 
 PHE   0.011   0.001   PHE A 366 
 TRP   0.012   0.001   TRP B 252 
 HIS   0.002   0.000   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 5938)
  covalent geometry    : angle       0.61834 ( 8014)
  hydrogen bonds       : bond        0.02925 (  223)
  hydrogen bonds       : angle       5.28140 (  618)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 MET cc_start: 0.7014 (mpp) cc_final: 0.6767 (mpp)
REVERT: A  382 ARG cc_start: 0.6402 (tpt90) cc_final: 0.5869 (tmt-80)
REVERT: A  402 MET cc_start: 0.7356 (mtm) cc_final: 0.6920 (ptp)
REVERT: B  196 MET cc_start: 0.8768 (mmm) cc_final: 0.8539 (mmm)
REVERT: H   21 MET cc_start: 0.8818 (mtp) cc_final: 0.8257 (mtm)
REVERT: H   38 ASN cc_start: 0.6761 (t0) cc_final: 0.6352 (t0)
  outliers start: 12
  outliers final: 10
  residues processed: 95
  average time/residue: 0.0940
  time to fit residues: 11.4602
Evaluate side-chains
  94 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 PHE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain B residue  367 SER
Chi-restraints excluded: chain C residue  157 GLU
Chi-restraints excluded: chain H residue   17 TYR
Chi-restraints excluded: chain H residue   32 LEU
Chi-restraints excluded: chain H residue   58 LEU
Chi-restraints excluded: chain H residue  116 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 24 optimal weight:    8.9990
   chunk 64 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 44 optimal weight:    0.1980
   chunk 67 optimal weight:    0.0270
   chunk 8 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.8040

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

Flipped N/Q/H residues before XYZ refinement:
** B 255 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 = 0.4800 r_free = 0.4800 target = 0.158982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.117791 restraints weight = 14415.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.121851 restraints weight = 8618.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.124758 restraints weight = 6063.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.126831 restraints weight = 4716.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.128515 restraints weight = 3905.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.4364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6287
moved from start:          0.3350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   5938  Z= 0.133
  Angle     :  0.653  10.080   8014  Z= 0.349
  Chirality :  0.044   0.251    900
  Planarity :  0.003   0.035   1038
  Dihedral  :  4.339  19.102    798
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.46 %
    Favored  : 82.35 %
  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 (0.32), residues: 737
  helix:  0.82 (0.33), residues: 260
  sheet: -1.08 (0.52), residues: 89
  loop : -0.88 (0.34), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 350 
 TYR   0.014   0.002   TYR H  17 
 PHE   0.012   0.001   PHE A 366 
 TRP   0.011   0.001   TRP B 252 
 HIS   0.002   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5938)
  covalent geometry    : angle       0.65256 ( 8014)
  hydrogen bonds       : bond        0.03213 (  223)
  hydrogen bonds       : angle       5.42630 (  618)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  382 ARG cc_start: 0.6502 (tpt90) cc_final: 0.6098 (tmt-80)
REVERT: A  402 MET cc_start: 0.7337 (mtm) cc_final: 0.6854 (ptp)
REVERT: H   21 MET cc_start: 0.8822 (mtp) cc_final: 0.8256 (mtp)
REVERT: H   38 ASN cc_start: 0.6680 (t0) cc_final: 0.6261 (t0)
  outliers start: 13
  outliers final: 11
  residues processed: 91
  average time/residue: 0.0795
  time to fit residues: 9.3278
Evaluate side-chains
  93 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 PHE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain B residue  367 SER
Chi-restraints excluded: chain C residue  157 GLU
Chi-restraints excluded: chain H residue   17 TYR
Chi-restraints excluded: chain H residue   32 LEU
Chi-restraints excluded: chain H residue   43 LEU
Chi-restraints excluded: chain H residue   58 LEU
Chi-restraints excluded: chain H residue  116 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 73 optimal weight:    8.9990
   chunk 57 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   chunk 1 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
B 161 GLN
** B 255 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 = 0.4795 r_free = 0.4795 target = 0.158530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.117675 restraints weight = 14561.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.121722 restraints weight = 8793.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.124673 restraints weight = 6192.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.126642 restraints weight = 4812.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.128314 restraints weight = 4004.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.4319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6336
moved from start:          0.3496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   5938  Z= 0.147
  Angle     :  0.671   9.503   8014  Z= 0.354
  Chirality :  0.045   0.248    900
  Planarity :  0.003   0.035   1038
  Dihedral  :  4.438  18.911    798
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 15.63 %
    Favored  : 82.35 %
  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 (0.32), residues: 737
  helix:  0.74 (0.33), residues: 261
  sheet: -1.16 (0.51), residues: 90
  loop : -0.89 (0.34), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 350 
 TYR   0.015   0.002   TYR H  17 
 PHE   0.012   0.002   PHE A 366 
 TRP   0.012   0.001   TRP B 252 
 HIS   0.002   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 5938)
  covalent geometry    : angle       0.67060 ( 8014)
  hydrogen bonds       : bond        0.03248 (  223)
  hydrogen bonds       : angle       5.50930 (  618)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  382 ARG cc_start: 0.6531 (tpt90) cc_final: 0.6122 (tmt-80)
REVERT: A  402 MET cc_start: 0.7286 (mtm) cc_final: 0.6820 (ptp)
REVERT: H   21 MET cc_start: 0.8794 (mtp) cc_final: 0.8252 (mtp)
REVERT: H   38 ASN cc_start: 0.6695 (t0) cc_final: 0.6279 (t0)
  outliers start: 12
  outliers final: 11
  residues processed: 91
  average time/residue: 0.0762
  time to fit residues: 9.0586
Evaluate side-chains
  95 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 PHE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain B residue  367 SER
Chi-restraints excluded: chain C residue  157 GLU
Chi-restraints excluded: chain H residue   17 TYR
Chi-restraints excluded: chain H residue   32 LEU
Chi-restraints excluded: chain H residue   43 LEU
Chi-restraints excluded: chain H residue   58 LEU
Chi-restraints excluded: chain H residue  116 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 73 optimal weight:   10.0000
   chunk 21 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 255 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 = 0.4803 r_free = 0.4803 target = 0.157781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.117310 restraints weight = 14067.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.121374 restraints weight = 8374.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.124290 restraints weight = 5841.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.126389 restraints weight = 4507.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.128016 restraints weight = 3722.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.4340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6315
moved from start:          0.3577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   5938  Z= 0.133
  Angle     :  0.676   9.577   8014  Z= 0.353
  Chirality :  0.046   0.247    900
  Planarity :  0.003   0.036   1038
  Dihedral  :  4.396  19.182    798
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 15.97 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.32), residues: 737
  helix:  0.76 (0.33), residues: 260
  sheet: -1.12 (0.51), residues: 89
  loop : -0.90 (0.34), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 350 
 TYR   0.015   0.001   TYR H  17 
 PHE   0.026   0.002   PHE A 186 
 TRP   0.012   0.001   TRP B 252 
 HIS   0.002   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5938)
  covalent geometry    : angle       0.67573 ( 8014)
  hydrogen bonds       : bond        0.03166 (  223)
  hydrogen bonds       : angle       5.46925 (  618)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1767.87 seconds
wall clock time: 31 minutes 3.55 seconds (1863.55 seconds total)