Starting phenix.real_space_refine
on Thu Feb 13 00:03:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e9w_27966/02_2025/8e9w_27966.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e9w_27966/02_2025/8e9w_27966.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e9w_27966/02_2025/8e9w_27966.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e9w_27966/02_2025/8e9w_27966.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e9w_27966/02_2025/8e9w_27966.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e9w_27966/02_2025/8e9w_27966.cif"
  }
  resolution = 2.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.021
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      56      5.16       5
     C    5451      2.51       5
     N    1450      2.21       5
     O    1572      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8529
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2187
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 9, 'TRANS': 270}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 76
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "B"
      Number of atoms: 1669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1669
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 4, 'TRANS': 208}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 80
          Unresolved non-hydrogen angles: 94
          Unresolved non-hydrogen dihedrals: 68
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 50
    Chain: "C"
      Number of atoms: 2505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2505
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 102
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 6, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 72
    Chain: "D"
      Number of atoms: 405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 405
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "E"
      Number of atoms: 1741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1741
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'WEC': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.79, per 1000 atoms: 0.68
  Number of scatterers: 8529
  At special positions: 0
  Unit cell: (116.16, 104.72, 124.08, 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      56     16.00
     O    1572      8.00
     N    1450      7.00
     C    5451      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 141 " - pdb=" SG  CYS A 221 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 517 " - pdb=" SG  CYS A 520 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.39
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2106

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 12 sheets defined
      37.4% alpha, 22.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 64 through 96
      removed outlier: 5.436A  pdb=" N   PHE A  70 " --> pdb=" O   TRP A  66 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   ILE A  71 " --> pdb=" O   GLN A  67 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   LYS A  94 " --> pdb=" O   ILE A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 100
    Processing helix  chain 'A' and resid 104 through 120
    Processing helix  chain 'A' and resid 121 through 131
      removed outlier: 3.656A  pdb=" N   ILE A 130 " --> pdb=" O   THR A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 172
      removed outlier: 4.046A  pdb=" N   TRP A 144 " --> pdb=" O   ALA A 140 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ASN A 153 " --> pdb=" O   CYS A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 180
    Processing helix  chain 'A' and resid 181 through 198
      removed outlier: 3.524A  pdb=" N   MET A 188 " --> pdb=" O   ARG A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 206
    Processing helix  chain 'A' and resid 230 through 240
    Processing helix  chain 'A' and resid 240 through 265
    Processing helix  chain 'A' and resid 487 through 496
      removed outlier: 3.858A  pdb=" N   GLN A 491 " --> pdb=" O   LYS A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 517
      Proline residue:  A 506  - end of helix
      removed outlier: 3.956A  pdb=" N   LEU A 512 " --> pdb=" O   ASN A 508 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   PHE A 516 " --> pdb=" O   LEU A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 544
      removed outlier: 3.978A  pdb=" N   TYR A 534 " --> pdb=" O   TYR A 530 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ASN A 536 " --> pdb=" O   LEU A 532 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   SER A 537 " --> pdb=" O   CYS A 533 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   THR A 538 " --> pdb=" O   TYR A 534 " (cutoff:3.500A)
      Proline residue:  A 541  - end of helix
    Processing helix  chain 'A' and resid 548 through 561
    Processing helix  chain 'B' and resid 6 through 32
      removed outlier: 3.532A  pdb=" N   LYS B  29 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 45
      removed outlier: 4.329A  pdb=" N   GLY B  45 " --> pdb=" O   ASP B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 101
      removed outlier: 4.106A  pdb=" N   GLN B  98 " --> pdb=" O   LYS B  95 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ASN B 101 " --> pdb=" O   GLN B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 130
    Processing helix  chain 'B' and resid 131 through 135
      removed outlier: 4.235A  pdb=" N   ARG B 135 " --> pdb=" O   ARG B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 154
      removed outlier: 3.645A  pdb=" N   LEU B 149 " --> pdb=" O   LYS B 145 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU B 154 " --> pdb=" O   ALA B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 168
    Processing helix  chain 'B' and resid 184 through 204
      removed outlier: 3.596A  pdb=" N   ILE B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   SER B 204 " --> pdb=" O   ILE B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 243
    Processing helix  chain 'C' and resid 3 through 24
      removed outlier: 3.515A  pdb=" N   LEU C   7 " --> pdb=" O   GLU C   3 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'C' and resid 128 through 132
      removed outlier: 4.107A  pdb=" N   GLY C 131 " --> pdb=" O   THR C 128 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ASN C 132 " --> pdb=" O   ARG C 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 128 through 132'
    Processing helix  chain 'D' and resid 6 through 24
    Processing helix  chain 'D' and resid 29 through 44
    Processing helix  chain 'E' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 75
      removed outlier: 6.427A  pdb=" N   LEU B  34 " --> pdb=" O   HIS B  82 " (cutoff:3.500A)
      removed outlier: 7.700A  pdb=" N   PHE B  84 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   LEU B  36 " --> pdb=" O   PHE B  84 " (cutoff:3.500A)
      removed outlier: 8.339A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 8.016A  pdb=" N   LEU B  38 " --> pdb=" O   VAL B  86 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ALA B 105 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ILE B 106 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   PHE B 142 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   PHE B 108 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   ASN B 144 " --> pdb=" O   PHE B 108 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   VAL B 110 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51
      removed outlier: 6.791A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.615A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.853A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151
      removed outlier: 4.387A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.623A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 3.697A  pdb=" N   MET C 262 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
      removed outlier: 5.778A  pdb=" N   ASP C 254 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 5.838A  pdb=" N   GLU C 260 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.746A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.045A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 129
    Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136
      removed outlier: 3.516A  pdb=" N   GLU E 234 " --> pdb=" O   VAL E 135 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   GLY E 213 " --> pdb=" O   LEU E 233 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   LEU E 162 " --> pdb=" O   TYR E 178 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   TYR E 178 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)

    423 hydrogen bonds defined for protein.
    1197 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: 3.09

  Time building geometry restraints manager: 2.74 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1621
        1.33 -     1.45: 2253
        1.45 -     1.57: 4760
        1.57 -     1.69: 1
        1.69 -     1.81: 78
  Bond restraints: 8713
  Sorted by residual:
  bond pdb=" C01 WEC A 601 "
       pdb=" N02 WEC A 601 "
    ideal  model  delta    sigma   weight residual
    1.455  1.286  0.169 2.00e-02 2.50e+03 7.13e+01
  bond pdb=" C06 WEC A 601 "
       pdb=" N07 WEC A 601 "
    ideal  model  delta    sigma   weight residual
    1.292  1.452 -0.160 2.00e-02 2.50e+03 6.37e+01
  bond pdb=" C06 WEC A 601 "
       pdb=" N05 WEC A 601 "
    ideal  model  delta    sigma   weight residual
    1.373  1.499 -0.126 2.00e-02 2.50e+03 4.00e+01
  bond pdb=" C03 WEC A 601 "
       pdb=" N02 WEC A 601 "
    ideal  model  delta    sigma   weight residual
    1.461  1.371  0.090 2.00e-02 2.50e+03 2.04e+01
  bond pdb=" C22 WEC A 601 "
       pdb=" N02 WEC A 601 "
    ideal  model  delta    sigma   weight residual
    1.459  1.372  0.087 2.00e-02 2.50e+03 1.91e+01
  ... (remaining 8708 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 11632
        1.92 -     3.84: 185
        3.84 -     5.77: 35
        5.77 -     7.69: 8
        7.69 -     9.61: 5
  Bond angle restraints: 11865
  Sorted by residual:
  angle pdb=" N   PHE B 167 "
        pdb=" CA  PHE B 167 "
        pdb=" C   PHE B 167 "
      ideal   model   delta    sigma   weight residual
     113.18  103.57    9.61 1.21e+00 6.83e-01 6.31e+01
  angle pdb=" CA  TYR E 223 "
        pdb=" C   TYR E 223 "
        pdb=" N   PRO E 224 "
      ideal   model   delta    sigma   weight residual
     118.03  125.61   -7.58 1.19e+00 7.06e-01 4.06e+01
  angle pdb=" CA  TYR E 223 "
        pdb=" C   TYR E 223 "
        pdb=" O   TYR E 223 "
      ideal   model   delta    sigma   weight residual
     120.23  113.82    6.41 1.02e+00 9.61e-01 3.95e+01
  angle pdb=" N   PRO B 184 "
        pdb=" CA  PRO B 184 "
        pdb=" C   PRO B 184 "
      ideal   model   delta    sigma   weight residual
     113.53  105.08    8.45 1.39e+00 5.18e-01 3.70e+01
  angle pdb=" O   PHE B 164 "
        pdb=" C   PHE B 164 "
        pdb=" N   PRO B 165 "
      ideal   model   delta    sigma   weight residual
     120.83  114.42    6.41 1.06e+00 8.90e-01 3.66e+01
  ... (remaining 11860 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 4671
       17.34 -    34.67: 358
       34.67 -    52.01: 60
       52.01 -    69.34: 11
       69.34 -    86.68: 4
  Dihedral angle restraints: 5104
    sinusoidal: 1844
      harmonic: 3260
  Sorted by residual:
  dihedral pdb=" CB  CYS A 517 "
           pdb=" SG  CYS A 517 "
           pdb=" SG  CYS A 520 "
           pdb=" CB  CYS A 520 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -168.18   82.18     1      1.00e+01 1.00e-02 8.29e+01
  dihedral pdb=" CB  CYS E 147 "
           pdb=" SG  CYS E 147 "
           pdb=" SG  CYS E 217 "
           pdb=" CB  CYS E 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  147.71  -54.71     1      1.00e+01 1.00e-02 4.05e+01
  dihedral pdb=" CB  CYS A 141 "
           pdb=" SG  CYS A 141 "
           pdb=" SG  CYS A 221 "
           pdb=" CB  CYS A 221 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -137.28   51.28     1      1.00e+01 1.00e-02 3.60e+01
  ... (remaining 5101 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1176
       0.059 -    0.118: 190
       0.118 -    0.177: 9
       0.177 -    0.236: 2
       0.236 -    0.295: 1
  Chirality restraints: 1378
  Sorted by residual:
  chirality pdb=" CA  THR B 171 "
            pdb=" N   THR B 171 "
            pdb=" C   THR B 171 "
            pdb=" CB  THR B 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.82   -0.30 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" CA  TYR E 223 "
            pdb=" N   TYR E 223 "
            pdb=" C   TYR E 223 "
            pdb=" CB  TYR E 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CA  ARG B 169 "
            pdb=" N   ARG B 169 "
            pdb=" C   ARG B 169 "
            pdb=" CB  ARG B 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.44e-01
  ... (remaining 1375 not shown)

  Planarity restraints: 1497
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 171 "    0.018 2.00e-02 2.50e+03   3.59e-02 1.29e+01
        pdb=" C   THR B 171 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   THR B 171 "    0.023 2.00e-02 2.50e+03
        pdb=" N   THR B 172 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 183 "    0.016 2.00e-02 2.50e+03   3.13e-02 9.81e+00
        pdb=" C   LYS A 183 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   LYS A 183 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ARG A 184 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D  54 "   -0.027 5.00e-02 4.00e+02   4.09e-02 2.68e+00
        pdb=" N   PRO D  55 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO D  55 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO D  55 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1494 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 879
        2.75 -     3.29: 8307
        3.29 -     3.82: 14124
        3.82 -     4.36: 16892
        4.36 -     4.90: 29622
  Nonbonded interactions: 69824
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 512 "
            pdb=" OG1 THR A 515 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" OG1 THR A  82 "
            pdb=" OG1 THR A 538 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O   LEU A  88 "
            pdb=" OG  SER A  92 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OG  SER E 149 "
            pdb=" O   LYS E 151 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" NH1 ARG C  49 "
            pdb=" O   TYR C  85 "
     model   vdw
     2.243 3.120
  ... (remaining 69819 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.160
  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:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     23.500
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.380
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
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      :  0.005   0.169   8713  Z= 0.341
  Angle     :  0.628   9.611  11865  Z= 0.374
  Chirality :  0.043   0.295   1378
  Planarity :  0.003   0.041   1497
  Dihedral  : 12.691  86.677   2989
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.23 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.26), residues: 1103
  helix:  0.42 (0.27), residues: 377
  sheet:  0.92 (0.32), residues: 285
  loop : -0.49 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  82 
 HIS   0.002   0.001   HIS B  82 
 PHE   0.012   0.001   PHE C 234 
 TYR   0.016   0.001   TYR E 178 
 ARG   0.006   0.000   ARG C 219 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ASP cc_start: 0.7368 (m-30) cc_final: 0.7094 (m-30)
REVERT: B   99 CYS cc_start: 0.7800 (m) cc_final: 0.7497 (m)
REVERT: C   98 SER cc_start: 0.8314 (p) cc_final: 0.8111 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 168
  average time/residue: 1.0097
  time to fit residues: 182.8692
Evaluate side-chains
  156 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 86 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 99 optimal weight:    1.9990
   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 144 ASN
C 125 ASN
C 266 HIS
E 167 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.132425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.114106 restraints weight = 11801.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 1.78
r_work: 0.3375 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8713  Z= 0.276
  Angle     :  0.581   7.951  11865  Z= 0.307
  Chirality :  0.044   0.140   1378
  Planarity :  0.004   0.041   1497
  Dihedral  :  4.690  35.635   1224
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  9.35 %
    Favored  : 89.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.26), residues: 1103
  helix:  1.08 (0.27), residues: 401
  sheet:  0.67 (0.31), residues: 298
  loop : -0.26 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 169 
 HIS   0.003   0.001   HIS B 209 
 PHE   0.012   0.002   PHE B  74 
 TYR   0.023   0.001   TYR E 178 
 ARG   0.004   0.000   ARG C 219 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 172
  time to evaluate  : 0.930 
Fit side-chains
REVERT: A   88 LEU cc_start: 0.7775 (mp) cc_final: 0.7514 (mp)
REVERT: B   20 ASP cc_start: 0.7907 (m-30) cc_final: 0.7534 (m-30)
REVERT: B  128 ILE cc_start: 0.8399 (tp) cc_final: 0.8093 (tp)
REVERT: C   98 SER cc_start: 0.8553 (p) cc_final: 0.8251 (t)
REVERT: C  160 SER cc_start: 0.8273 (t) cc_final: 0.7908 (p)
REVERT: E   86 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8080 (pp)
REVERT: E  190 ARG cc_start: 0.8288 (ptt-90) cc_final: 0.7921 (ptt180)
  outliers start: 11
  outliers final: 4
  residues processed: 178
  average time/residue: 1.2109
  time to fit residues: 229.6705
Evaluate side-chains
  169 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 164
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  334 SER
Chi-restraints excluded: chain E residue   86 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 96 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 98 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 229 ASN
C 125 ASN
E 167 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.133099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.114537 restraints weight = 11840.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 1.80
r_work: 0.3385 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8713  Z= 0.241
  Angle     :  0.548   9.410  11865  Z= 0.287
  Chirality :  0.043   0.136   1378
  Planarity :  0.004   0.041   1497
  Dihedral  :  4.636  35.847   1224
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 12.88 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.26), residues: 1103
  helix:  1.21 (0.28), residues: 402
  sheet:  0.49 (0.31), residues: 295
  loop : -0.21 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 169 
 HIS   0.003   0.001   HIS B 209 
 PHE   0.013   0.001   PHE B  74 
 TYR   0.021   0.001   TYR E 178 
 ARG   0.006   0.000   ARG B  24 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 165
  time to evaluate  : 0.885 
Fit side-chains
REVERT: A   88 LEU cc_start: 0.7838 (mp) cc_final: 0.7603 (mp)
REVERT: B   20 ASP cc_start: 0.7862 (m-30) cc_final: 0.7521 (m-30)
REVERT: B   99 CYS cc_start: 0.8469 (m) cc_final: 0.8220 (m)
REVERT: B  166 GLU cc_start: 0.7966 (mp0) cc_final: 0.7712 (mp0)
REVERT: C   98 SER cc_start: 0.8575 (p) cc_final: 0.8179 (t)
REVERT: E  190 ARG cc_start: 0.8308 (ptt-90) cc_final: 0.7892 (ptt180)
  outliers start: 12
  outliers final: 6
  residues processed: 170
  average time/residue: 1.1448
  time to fit residues: 207.8340
Evaluate side-chains
  163 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 157
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  334 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
C 125 ASN
C 340 ASN
E 167 GLN
E 171 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.130841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.112302 restraints weight = 11750.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.79
r_work: 0.3356 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   8713  Z= 0.406
  Angle     :  0.624  14.613  11865  Z= 0.323
  Chirality :  0.046   0.136   1378
  Planarity :  0.004   0.042   1497
  Dihedral  :  4.995  40.233   1224
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 15.17 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.26), residues: 1103
  helix:  0.95 (0.27), residues: 403
  sheet:  0.37 (0.30), residues: 309
  loop : -0.36 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 169 
 HIS   0.005   0.001   HIS B 209 
 PHE   0.025   0.002   PHE A 225 
 TYR   0.021   0.002   TYR E 178 
 ARG   0.008   0.001   ARG C 219 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 171
  time to evaluate  : 0.956 
Fit side-chains
REVERT: B   20 ASP cc_start: 0.7845 (m-30) cc_final: 0.7507 (m-30)
REVERT: B   99 CYS cc_start: 0.8469 (m) cc_final: 0.8212 (m)
REVERT: B  166 GLU cc_start: 0.7974 (mp0) cc_final: 0.7671 (mp0)
REVERT: C   98 SER cc_start: 0.8601 (p) cc_final: 0.8188 (t)
REVERT: E  190 ARG cc_start: 0.8301 (ptt-90) cc_final: 0.7876 (ptt180)
  outliers start: 22
  outliers final: 14
  residues processed: 179
  average time/residue: 1.2069
  time to fit residues: 230.3095
Evaluate side-chains
  182 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 168
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  542 VAL
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain C residue   74 SER
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  334 SER
Chi-restraints excluded: chain E residue  143 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0000
   chunk 5 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 104 optimal weight:    1.9990
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
C 239 ASN
E 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.132692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.114169 restraints weight = 11746.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.78
r_work: 0.3387 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8713  Z= 0.223
  Angle     :  0.549  12.144  11865  Z= 0.284
  Chirality :  0.043   0.188   1378
  Planarity :  0.004   0.041   1497
  Dihedral  :  4.678  35.160   1224
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.08 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.26), residues: 1103
  helix:  1.26 (0.27), residues: 403
  sheet:  0.39 (0.30), residues: 297
  loop : -0.29 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 169 
 HIS   0.003   0.001   HIS B 209 
 PHE   0.019   0.001   PHE A 225 
 TYR   0.024   0.001   TYR E 178 
 ARG   0.007   0.000   ARG C 219 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 167
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ASP cc_start: 0.7848 (m-30) cc_final: 0.7516 (m-30)
REVERT: B   99 CYS cc_start: 0.8422 (m) cc_final: 0.8177 (m)
REVERT: C   98 SER cc_start: 0.8578 (p) cc_final: 0.8148 (t)
REVERT: C  293 ASN cc_start: 0.8253 (p0) cc_final: 0.8029 (p0)
REVERT: E  190 ARG cc_start: 0.8278 (ptt-90) cc_final: 0.8007 (ptt180)
  outliers start: 23
  outliers final: 12
  residues processed: 178
  average time/residue: 1.1902
  time to fit residues: 225.7782
Evaluate side-chains
  179 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 167
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain C residue   74 SER
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  334 SER
Chi-restraints excluded: chain D residue   42 GLU
Chi-restraints excluded: chain E residue  143 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0050
   chunk 82 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 104 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 99 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   chunk 84 optimal weight:    0.4980
   chunk 83 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.6394

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

Flipped N/Q/H residues before XYZ refinement:
A  86 ASN
B 244 ASN
C 110 ASN
C 295 ASN
E 167 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.132508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.114015 restraints weight = 11671.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 1.78
r_work: 0.3383 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8713  Z= 0.232
  Angle     :  0.547  11.889  11865  Z= 0.284
  Chirality :  0.043   0.182   1378
  Planarity :  0.004   0.041   1497
  Dihedral  :  4.663  34.933   1224
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 17.33 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.26), residues: 1103
  helix:  1.34 (0.27), residues: 403
  sheet:  0.33 (0.31), residues: 293
  loop : -0.21 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 169 
 HIS   0.003   0.001   HIS B 209 
 PHE   0.018   0.001   PHE A 225 
 TYR   0.023   0.001   TYR E 178 
 ARG   0.006   0.000   ARG B  24 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 166
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ASP cc_start: 0.7851 (m-30) cc_final: 0.7593 (m-30)
REVERT: B   99 CYS cc_start: 0.8411 (m) cc_final: 0.8164 (m)
REVERT: B  147 ASP cc_start: 0.8160 (p0) cc_final: 0.7358 (p0)
REVERT: B  151 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6014 (mp0)
REVERT: C   57 LYS cc_start: 0.8375 (mtpt) cc_final: 0.8133 (mtpt)
REVERT: C   98 SER cc_start: 0.8577 (p) cc_final: 0.8148 (t)
REVERT: E   87 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7860 (ptt90)
REVERT: E  190 ARG cc_start: 0.8272 (ptt-90) cc_final: 0.7855 (ptt180)
  outliers start: 22
  outliers final: 15
  residues processed: 174
  average time/residue: 1.2273
  time to fit residues: 227.6438
Evaluate side-chains
  181 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 164
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  151 GLU
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain C residue   74 SER
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  334 SER
Chi-restraints excluded: chain D residue   42 GLU
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  162 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0060
   chunk 23 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 105 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
B 244 ASN
E 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.132532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.113954 restraints weight = 11840.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 1.81
r_work: 0.3390 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8713  Z= 0.226
  Angle     :  0.548  11.042  11865  Z= 0.284
  Chirality :  0.043   0.185   1378
  Planarity :  0.004   0.041   1497
  Dihedral  :  4.620  34.239   1224
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 16.99 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.26), residues: 1103
  helix:  1.39 (0.28), residues: 403
  sheet:  0.36 (0.30), residues: 303
  loop : -0.19 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 169 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.017   0.001   PHE A 225 
 TYR   0.021   0.001   TYR E 178 
 ARG   0.005   0.000   ARG C 219 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 165
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ASP cc_start: 0.7843 (m-30) cc_final: 0.7567 (m-30)
REVERT: B   99 CYS cc_start: 0.8403 (m) cc_final: 0.8156 (m)
REVERT: B  147 ASP cc_start: 0.8170 (p0) cc_final: 0.7341 (p0)
REVERT: B  151 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6041 (mp0)
REVERT: B  166 GLU cc_start: 0.7961 (mp0) cc_final: 0.7577 (mp0)
REVERT: C   57 LYS cc_start: 0.8374 (mtpt) cc_final: 0.8132 (mtpt)
REVERT: C   98 SER cc_start: 0.8580 (p) cc_final: 0.8145 (t)
REVERT: C  258 ASP cc_start: 0.7694 (t0) cc_final: 0.7442 (t0)
REVERT: E   86 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8160 (pp)
REVERT: E  190 ARG cc_start: 0.8271 (ptt-90) cc_final: 0.7851 (ptt180)
  outliers start: 29
  outliers final: 18
  residues processed: 178
  average time/residue: 1.2155
  time to fit residues: 230.9584
Evaluate side-chains
  182 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 162
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  256 LYS
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  542 VAL
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  151 GLU
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain C residue   74 SER
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  334 SER
Chi-restraints excluded: chain D residue   42 GLU
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  198 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0370
   chunk 96 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0870
   chunk 17 optimal weight:    0.6980
   chunk 81 optimal weight:    0.0970
   overall best weight:    0.3434

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

Flipped N/Q/H residues before XYZ refinement:
B 244 ASN
C 340 ASN
E 167 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.134319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.115737 restraints weight = 11931.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 1.82
r_work: 0.3411 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8713  Z= 0.162
  Angle     :  0.516   8.617  11865  Z= 0.268
  Chirality :  0.042   0.162   1378
  Planarity :  0.003   0.041   1497
  Dihedral  :  4.431  32.236   1224
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 17.67 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.26), residues: 1103
  helix:  1.56 (0.28), residues: 402
  sheet:  0.37 (0.31), residues: 287
  loop : -0.13 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 169 
 HIS   0.002   0.001   HIS E  35 
 PHE   0.015   0.001   PHE A 225 
 TYR   0.022   0.001   TYR E 178 
 ARG   0.008   0.000   ARG C 219 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 167
  time to evaluate  : 1.100 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ASP cc_start: 0.7849 (m-30) cc_final: 0.7554 (m-30)
REVERT: B   99 CYS cc_start: 0.8391 (m) cc_final: 0.8139 (m)
REVERT: B  147 ASP cc_start: 0.8163 (p0) cc_final: 0.7324 (p0)
REVERT: B  151 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.5967 (mp0)
REVERT: C   57 LYS cc_start: 0.8323 (mtpt) cc_final: 0.8059 (mtpt)
REVERT: C   98 SER cc_start: 0.8566 (p) cc_final: 0.8151 (t)
REVERT: C  258 ASP cc_start: 0.7650 (t0) cc_final: 0.7356 (t0)
REVERT: E  211 ASP cc_start: 0.7914 (t0) cc_final: 0.7666 (m-30)
  outliers start: 28
  outliers final: 13
  residues processed: 179
  average time/residue: 1.0731
  time to fit residues: 206.3556
Evaluate side-chains
  185 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 171
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  151 GLU
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain C residue   74 SER
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  334 SER
Chi-restraints excluded: chain D residue   42 GLU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  198 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 101 optimal weight:    2.9990
   chunk 108 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0270
   chunk 69 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0670
   chunk 17 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 6 optimal weight:    9.9990
   overall best weight:    0.3976

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

Flipped N/Q/H residues before XYZ refinement:
B 244 ASN
C 125 ASN
C 295 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.134260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.115709 restraints weight = 11860.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 1.81
r_work: 0.3409 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8713  Z= 0.175
  Angle     :  0.523   8.549  11865  Z= 0.273
  Chirality :  0.042   0.157   1378
  Planarity :  0.004   0.049   1497
  Dihedral  :  4.403  32.394   1224
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 18.02 %
    Favored  : 79.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.26), residues: 1103
  helix:  1.60 (0.28), residues: 402
  sheet:  0.46 (0.30), residues: 296
  loop : -0.12 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 169 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.015   0.001   PHE A 225 
 TYR   0.021   0.001   TYR E 178 
 ARG   0.013   0.000   ARG B  24 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 173
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ASP cc_start: 0.7855 (m-30) cc_final: 0.7579 (m-30)
REVERT: B   99 CYS cc_start: 0.8390 (m) cc_final: 0.8153 (m)
REVERT: B  147 ASP cc_start: 0.8160 (p0) cc_final: 0.7321 (p0)
REVERT: B  151 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.5978 (mp0)
REVERT: B  166 GLU cc_start: 0.7911 (mp0) cc_final: 0.7493 (mp0)
REVERT: C   57 LYS cc_start: 0.8319 (mtpt) cc_final: 0.8039 (mtpt)
REVERT: C   98 SER cc_start: 0.8562 (p) cc_final: 0.8149 (t)
REVERT: C  258 ASP cc_start: 0.7667 (t0) cc_final: 0.7328 (t0)
REVERT: E  137 VAL cc_start: 0.8310 (t) cc_final: 0.8001 (p)
REVERT: E  211 ASP cc_start: 0.7910 (t0) cc_final: 0.7696 (m-30)
  outliers start: 23
  outliers final: 15
  residues processed: 183
  average time/residue: 1.0631
  time to fit residues: 208.8506
Evaluate side-chains
  187 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 171
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  256 LYS
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  151 GLU
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain C residue   74 SER
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  334 SER
Chi-restraints excluded: chain D residue   42 GLU
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  198 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 55 optimal weight:    0.4980
   chunk 96 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 46 optimal weight:    0.0470
   chunk 16 optimal weight:    0.3980
   chunk 36 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 98 optimal weight:    0.9990
   chunk 91 optimal weight:    0.2980
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
B 244 ASN
C 110 ASN
C 295 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.134047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.115532 restraints weight = 11763.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 1.80
r_work: 0.3411 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3261 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8713  Z= 0.183
  Angle     :  0.530   9.257  11865  Z= 0.277
  Chirality :  0.042   0.165   1378
  Planarity :  0.004   0.050   1497
  Dihedral  :  4.436  32.308   1224
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 19.61 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.26), residues: 1103
  helix:  1.61 (0.28), residues: 401
  sheet:  0.44 (0.31), residues: 286
  loop : -0.14 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 169 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.015   0.001   PHE A 225 
 TYR   0.020   0.001   TYR E 178 
 ARG   0.012   0.000   ARG B  24 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 160
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ASP cc_start: 0.7871 (m-30) cc_final: 0.7588 (m-30)
REVERT: B   99 CYS cc_start: 0.8376 (m) cc_final: 0.8136 (m)
REVERT: B  147 ASP cc_start: 0.8118 (p0) cc_final: 0.7309 (p0)
REVERT: B  151 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.5996 (mp0)
REVERT: B  200 ILE cc_start: 0.7690 (mt) cc_final: 0.7450 (mp)
REVERT: C   57 LYS cc_start: 0.8324 (mtpt) cc_final: 0.8026 (mtpt)
REVERT: C   98 SER cc_start: 0.8567 (p) cc_final: 0.8154 (t)
REVERT: C  258 ASP cc_start: 0.7678 (t0) cc_final: 0.7314 (t0)
REVERT: E  137 VAL cc_start: 0.8304 (t) cc_final: 0.8010 (p)
REVERT: E  211 ASP cc_start: 0.7900 (t0) cc_final: 0.7678 (m-30)
  outliers start: 19
  outliers final: 16
  residues processed: 170
  average time/residue: 1.0274
  time to fit residues: 187.9835
Evaluate side-chains
  174 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  256 LYS
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  542 VAL
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  151 GLU
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain C residue   74 SER
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  334 SER
Chi-restraints excluded: chain D residue   42 GLU
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  198 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 55 optimal weight:    0.4980
   chunk 91 optimal weight:    0.0970
   chunk 14 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 52 optimal weight:    0.1980
   chunk 107 optimal weight:    0.6980
   chunk 86 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
B 144 ASN
B 244 ASN
C 125 ASN
C 295 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.134159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.115514 restraints weight = 11833.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 1.82
r_work: 0.3409 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8713  Z= 0.185
  Angle     :  0.533   9.268  11865  Z= 0.278
  Chirality :  0.042   0.146   1378
  Planarity :  0.004   0.047   1497
  Dihedral  :  4.408  32.325   1224
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 19.27 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.26), residues: 1103
  helix:  1.66 (0.28), residues: 401
  sheet:  0.46 (0.30), residues: 296
  loop : -0.14 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 134 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.015   0.001   PHE A 225 
 TYR   0.020   0.001   TYR E 178 
 ARG   0.011   0.000   ARG B  24 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7395.38 seconds
wall clock time: 130 minutes 57.24 seconds (7857.24 seconds total)