Starting phenix.real_space_refine
on Tue Feb 13 21:10:22 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6r_35204/02_2024/8i6r_35204_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6r_35204/02_2024/8i6r_35204.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6r_35204/02_2024/8i6r_35204.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6r_35204/02_2024/8i6r_35204.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6r_35204/02_2024/8i6r_35204_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6r_35204/02_2024/8i6r_35204_updated.pdb"
  }
  resolution = 4.0
  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=   0.002 sd=   0.031
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      1      5.21       5
     S      20      5.16       5
     C    5027      2.51       5
     N    1275      2.21       5
     O    1428      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  237": "OE1" <-> "OE2"
    Residue "A PHE  296": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   11": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   23": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  292": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 7757
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2210
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2210
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 11, 'TRANS': 277}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'ARG:plan': 20}
          Unresolved non-hydrogen planarities: 41
    Chain: "B"
      Number of atoms: 1680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1680
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 10, 'TRANS': 211}
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'ARG:plan': 22}
          Unresolved non-hydrogen planarities: 44
    Chain: "C"
      Number of atoms: 2128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2128
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 9, 'TRANS': 268}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ARG:plan': 20}
          Unresolved non-hydrogen planarities: 40
    Chain: "D"
      Number of atoms: 1676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1676
          Classifications: {'peptide': 222}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 211}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 26
          Planarities with less than four sites: {'ARG:plan': 22}
          Unresolved non-hydrogen planarities: 44
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.51, per 1000 atoms: 0.58
  Number of scatterers: 7757
  At special positions: 0
  Unit cell: (67.782, 80.652, 145.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      20     16.00
     P       6     15.00
     Mg      1     11.99
     O    1428      8.00
     N    1275      7.00
     C    5027      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  - 3.50
        Amino acid           : False - 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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.27
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1834

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      35 helices and 4 sheets defined
      56.5% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 53
      removed outlier: 3.666A  pdb=" N   HIS A  41 " --> pdb=" O   TYR A  37 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA A  43 " --> pdb=" O   GLU A  39 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL A  46 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 85
      removed outlier: 3.685A  pdb=" N   LEU A  72 " --> pdb=" O   ILE A  68 " (cutoff:3.500A)
      Proline residue:  A  73  - end of helix
      removed outlier: 3.739A  pdb=" N   LEU A  79 " --> pdb=" O   GLY A  75 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU A  80 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 90
      No H-bonds generated for 'chain 'A' and resid 88 through 90'
    Processing helix  chain 'A' and resid 106 through 117
      removed outlier: 4.226A  pdb=" N   GLU A 114 " --> pdb=" O   GLN A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 140
      removed outlier: 3.598A  pdb=" N   SER A 135 " --> pdb=" O   GLU A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 180
    Processing helix  chain 'A' and resid 191 through 232
      removed outlier: 3.719A  pdb=" N   LYS A 202 " --> pdb=" O   SER A 198 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLY A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LEU A 217 " --> pdb=" O   ILE A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 244
    Processing helix  chain 'A' and resid 248 through 292
      Proline residue:  A 254  - end of helix
      removed outlier: 4.146A  pdb=" N   GLY A 283 " --> pdb=" O   ASN A 279 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   SER A 284 " --> pdb=" O   TRP A 280 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   VAL A 285 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   VAL A 286 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   ASN A 287 " --> pdb=" O   GLY A 283 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU A 288 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 331
      removed outlier: 3.837A  pdb=" N   HIS A 328 " --> pdb=" O   ALA A 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 48
      removed outlier: 3.570A  pdb=" N   ILE B  48 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 80
      Proline residue:  B  75  - end of helix
      removed outlier: 3.802A  pdb=" N   GLN B  80 " --> pdb=" O   PHE B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 106
      Proline residue:  B 103  - end of helix
    Processing helix  chain 'B' and resid 111 through 124
      removed outlier: 3.606A  pdb=" N   ALA B 115 " --> pdb=" O   LYS B 111 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   LYS B 116 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   GLU B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ARG B 124 " --> pdb=" O   SER B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 137
      No H-bonds generated for 'chain 'B' and resid 135 through 137'
    Processing helix  chain 'B' and resid 140 through 155
      removed outlier: 6.357A  pdb=" N   HIS B 154 " --> pdb=" O   ARG B 150 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   GLN B 155 " --> pdb=" O   ALA B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 185
    Processing helix  chain 'B' and resid 198 through 202
      removed outlier: 3.810A  pdb=" N   ARG B 202 " --> pdb=" O   ALA B 198 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 198 through 202'
    Processing helix  chain 'C' and resid 34 through 53
      removed outlier: 3.614A  pdb=" N   HIS C  41 " --> pdb=" O   TYR C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 85
      removed outlier: 3.743A  pdb=" N   VAL C  65 " --> pdb=" O   PHE C  61 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   MET C  66 " --> pdb=" O   THR C  62 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU C  72 " --> pdb=" O   ILE C  68 " (cutoff:3.500A)
      Proline residue:  C  73  - end of helix
    Processing helix  chain 'C' and resid 106 through 118
      removed outlier: 4.258A  pdb=" N   GLU C 114 " --> pdb=" O   GLN C 110 " (cutoff:3.500A)
      removed outlier: 4.829A  pdb=" N   GLN C 115 " --> pdb=" O   ASP C 111 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   ILE C 116 " --> pdb=" O   LEU C 112 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   GLU C 117 " --> pdb=" O   ARG C 113 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG C 118 " --> pdb=" O   GLU C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 171 through 178
    Processing helix  chain 'C' and resid 192 through 200
    Processing helix  chain 'C' and resid 203 through 232
    Processing helix  chain 'C' and resid 236 through 244
      removed outlier: 3.705A  pdb=" N   LYS C 242 " --> pdb=" O   ILE C 238 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   VAL C 244 " --> pdb=" O   VAL C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 248 through 291
      Proline residue:  C 254  - end of helix
      removed outlier: 3.586A  pdb=" N   TRP C 271 " --> pdb=" O   GLY C 267 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA C 272 " --> pdb=" O   ILE C 268 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   GLY C 283 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 5.420A  pdb=" N   SER C 284 " --> pdb=" O   TRP C 280 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   VAL C 285 " --> pdb=" O   LEU C 281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 303 through 331
      removed outlier: 3.585A  pdb=" N   SER C 308 " --> pdb=" O   ASP C 304 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ARG C 327 " --> pdb=" O   LEU C 323 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   HIS C 328 " --> pdb=" O   ALA C 324 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 42 through 49
      removed outlier: 3.846A  pdb=" N   ILE D  48 " --> pdb=" O   LEU D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 71 through 80
      Proline residue:  D  75  - end of helix
      removed outlier: 5.031A  pdb=" N   ARG D  79 " --> pdb=" O   PHE D  76 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLN D  80 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 96 through 107
      Proline residue:  D 103  - end of helix
    Processing helix  chain 'D' and resid 111 through 125
      removed outlier: 3.554A  pdb=" N   GLU D 123 " --> pdb=" O   ALA D 119 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ARG D 124 " --> pdb=" O   SER D 120 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   VAL D 125 " --> pdb=" O   ALA D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 137
      No H-bonds generated for 'chain 'D' and resid 135 through 137'
    Processing helix  chain 'D' and resid 140 through 155
      removed outlier: 3.800A  pdb=" N   GLN D 144 " --> pdb=" O   THR D 140 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   HIS D 154 " --> pdb=" O   ARG D 150 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   GLN D 155 " --> pdb=" O   ALA D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 184
      removed outlier: 3.692A  pdb=" N   SER D 174 " --> pdb=" O   PRO D 170 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   GLU D 175 " --> pdb=" O   ARG D 171 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ILE D 176 " --> pdb=" O   LEU D 172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 201
      removed outlier: 3.926A  pdb=" N   ALA D 201 " --> pdb=" O   ALA D 198 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 96 through 99
      removed outlier: 3.706A  pdb=" N   LEU A  98 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   SER A 160 " --> pdb=" O   GLN A 126 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 23 through 25
      removed outlier: 4.431A  pdb=" N   ARG B   3 " --> pdb=" O   LEU B  60 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   LEU B  60 " --> pdb=" O   ARG B   3 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 30 through 33
      removed outlier: 6.173A  pdb=" N   VAL B 190 " --> pdb=" O   LEU B  31 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   VAL B  33 " --> pdb=" O   VAL B 190 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ILE B 192 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  C
    Processing sheet with id=  D, first strand: chain 'D' and resid 190 through 193
      removed outlier: 3.572A  pdb=" N   ILE D 192 " --> pdb=" O   LEU D  31 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   LEU D 208 " --> pdb=" O   THR D  34 " (cutoff:3.500A)

    363 hydrogen bonds defined for protein.
    1056 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: 1.84

  Time building geometry restraints manager: 3.48 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: 2517
        1.34 -     1.46: 1318
        1.46 -     1.58: 4006
        1.58 -     1.69: 10
        1.69 -     1.81: 38
  Bond restraints: 7889
  Sorted by residual:
  bond pdb=" C6  ATP D 301 "
       pdb=" N6  ATP D 301 "
    ideal  model  delta    sigma   weight residual
    1.337  1.445 -0.108 1.10e-02 8.26e+03 9.66e+01
  bond pdb=" C6  ATP B 301 "
       pdb=" N6  ATP B 301 "
    ideal  model  delta    sigma   weight residual
    1.337  1.445 -0.108 1.10e-02 8.26e+03 9.60e+01
  bond pdb=" C5  ATP D 301 "
       pdb=" N7  ATP D 301 "
    ideal  model  delta    sigma   weight residual
    1.387  1.471 -0.084 1.00e-02 1.00e+04 6.99e+01
  bond pdb=" C5  ATP B 301 "
       pdb=" N7  ATP B 301 "
    ideal  model  delta    sigma   weight residual
    1.387  1.465 -0.078 1.00e-02 1.00e+04 6.07e+01
  bond pdb=" O5' ATP B 301 "
       pdb=" PA  ATP B 301 "
    ideal  model  delta    sigma   weight residual
    1.579  1.645 -0.066 1.10e-02 8.26e+03 3.55e+01
  ... (remaining 7884 not shown)

  Histogram of bond angle deviations from ideal:
       99.62 -   106.98: 241
      106.98 -   114.33: 4873
      114.33 -   121.69: 3864
      121.69 -   129.04: 1627
      129.04 -   136.40: 65
  Bond angle restraints: 10670
  Sorted by residual:
  angle pdb=" PB  ATP B 301 "
        pdb=" O3B ATP B 301 "
        pdb=" PG  ATP B 301 "
      ideal   model   delta    sigma   weight residual
     139.87  118.42   21.45 1.00e+00 1.00e+00 4.60e+02
  angle pdb=" PB  ATP D 301 "
        pdb=" O3B ATP D 301 "
        pdb=" PG  ATP D 301 "
      ideal   model   delta    sigma   weight residual
     139.87  120.57   19.30 1.00e+00 1.00e+00 3.73e+02
  angle pdb=" PA  ATP B 301 "
        pdb=" O3A ATP B 301 "
        pdb=" PB  ATP B 301 "
      ideal   model   delta    sigma   weight residual
     136.83  117.70   19.13 1.00e+00 1.00e+00 3.66e+02
  angle pdb=" PA  ATP D 301 "
        pdb=" O3A ATP D 301 "
        pdb=" PB  ATP D 301 "
      ideal   model   delta    sigma   weight residual
     136.83  121.83   15.00 1.00e+00 1.00e+00 2.25e+02
  angle pdb=" C4  ATP D 301 "
        pdb=" N9  ATP D 301 "
        pdb=" C8  ATP D 301 "
      ideal   model   delta    sigma   weight residual
     105.72  115.00   -9.28 1.00e+00 1.00e+00 8.61e+01
  ... (remaining 10665 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4267
       17.94 -    35.87: 424
       35.87 -    53.81: 84
       53.81 -    71.75: 23
       71.75 -    89.68: 6
  Dihedral angle restraints: 4804
    sinusoidal: 1952
      harmonic: 2852
  Sorted by residual:
  dihedral pdb=" CA  ILE D 216 "
           pdb=" C   ILE D 216 "
           pdb=" N   ALA D 217 "
           pdb=" CA  ALA D 217 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.65   27.35     0      5.00e+00 4.00e-02 2.99e+01
  dihedral pdb=" CA  ILE B 216 "
           pdb=" C   ILE B 216 "
           pdb=" N   ALA B 217 "
           pdb=" CA  ALA B 217 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.09   24.91     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" CG  ARG A 130 "
           pdb=" CD  ARG A 130 "
           pdb=" NE  ARG A 130 "
           pdb=" CZ  ARG A 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -24.85  -65.15     2      1.50e+01 4.44e-03 1.76e+01
  ... (remaining 4801 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 841
       0.035 -    0.070: 294
       0.070 -    0.105: 110
       0.105 -    0.140: 26
       0.140 -    0.175: 7
  Chirality restraints: 1278
  Sorted by residual:
  chirality pdb=" CB  ILE D   2 "
            pdb=" CA  ILE D   2 "
            pdb=" CG1 ILE D   2 "
            pdb=" CG2 ILE D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.18 2.00e-01 2.50e+01 7.68e-01
  chirality pdb=" C2' ATP D 301 "
            pdb=" C1' ATP D 301 "
            pdb=" C3' ATP D 301 "
            pdb=" O2' ATP D 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.51   -0.17 2.00e-01 2.50e+01 7.65e-01
  chirality pdb=" C2' ATP B 301 "
            pdb=" C1' ATP B 301 "
            pdb=" C3' ATP B 301 "
            pdb=" O2' ATP B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.51   -0.17 2.00e-01 2.50e+01 7.17e-01
  ... (remaining 1275 not shown)

  Planarity restraints: 1309
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 202 "    0.015 2.00e-02 2.50e+03   3.02e-02 9.12e+00
        pdb=" C   LYS C 202 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   LYS C 202 "    0.020 2.00e-02 2.50e+03
        pdb=" N   LEU C 203 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 192 "   -0.015 2.00e-02 2.50e+03   2.86e-02 8.19e+00
        pdb=" C   VAL A 192 "    0.050 2.00e-02 2.50e+03
        pdb=" O   VAL A 192 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   TRP A 193 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D 109 "   -0.035 5.00e-02 4.00e+02   5.33e-02 4.54e+00
        pdb=" N   PRO D 110 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO D 110 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO D 110 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1306 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.42: 53
        2.42 -     3.04: 5433
        3.04 -     3.66: 12930
        3.66 -     4.28: 17466
        4.28 -     4.90: 26631
  Nonbonded interactions: 62513
  Sorted by model distance:
  nonbonded pdb=" O1B ATP B 301 "
            pdb="MG    MG B 302 "
     model   vdw
     1.797 2.170
  nonbonded pdb=" O2B ATP B 301 "
            pdb="MG    MG B 302 "
     model   vdw
     1.963 2.170
  nonbonded pdb=" O   ILE C  68 "
            pdb=" OG  SER C  71 "
     model   vdw
     2.120 2.440
  nonbonded pdb=" NE2 GLN A  95 "
            pdb=" OE2 GLU A 124 "
     model   vdw
     2.148 2.520
  nonbonded pdb=" O   ARG C  92 "
            pdb=" NE2 GLN C  95 "
     model   vdw
     2.166 2.520
  ... (remaining 62508 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 35 through 131 or resid 157 through 335))
  selection = (chain 'C' and (resid 35 through 249 or (resid 250 and (name N or name CA or nam \ 
e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name  \ 
CE2 or name CZ )) or resid 251 through 335))
}
ncs_group {
  reference = (chain 'B' and (resid 1 through 8 or (resid 9 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 10 through 222 or resid 301))
  selection = chain 'D'
}

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:             2.620
  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:          7.100
  Check model and map are aligned:         0.110
  Set scattering table:                    0.070
  Process input model:                     23.350
  Find NCS groups from input model:        0.440
  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:             0.010
  Load rotamer database and sin/cos tables:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
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      :  0.006   0.108   7889  Z= 0.414
  Angle     :  1.029  21.451  10670  Z= 0.672
  Chirality :  0.043   0.175   1278
  Planarity :  0.005   0.053   1309
  Dihedral  : 15.432  89.684   2970
  Min Nonbonded Distance : 1.797

Molprobity Statistics.
  All-atom Clashscore : 22.17
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.81 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  1.55 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.44 (0.27), residues: 999
  helix:  1.19 (0.22), residues: 568
  sheet: -2.34 (0.49), residues: 89
  loop : -2.30 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP C 322 
 HIS   0.006   0.001   HIS D  88 
 PHE   0.017   0.002   PHE B 180 
 TYR   0.013   0.002   TYR D  11 
 ARG   0.000   0.000   ARG B 171 

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4617 (tpp) cc_final: 0.4203 (tpp)
REVERT: D   85 PHE cc_start: 0.9092 (m-80) cc_final: 0.8672 (m-80)
REVERT: D   87 ASN cc_start: 0.9616 (t0) cc_final: 0.9407 (t0)
REVERT: D  109 MET cc_start: 0.8676 (mmt) cc_final: 0.8186 (mmm)
REVERT: D  160 LEU cc_start: 0.9731 (mt) cc_final: 0.9519 (tt)
REVERT: D  207 MET cc_start: 0.7413 (mpp) cc_final: 0.6937 (mpp)
  outliers start: 14
  outliers final: 14
  residues processed: 85
  average time/residue: 0.1477
  time to fit residues: 18.7505
Evaluate side-chains
  65 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  118 ARG
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  175 ARG
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  118 ARG
Chi-restraints excluded: chain C residue  168 ARG
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue  124 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    0.0670
   chunk 75 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 50 optimal weight:    9.9990
   chunk 40 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 57 optimal weight:   30.0000
   chunk 89 optimal weight:    0.0370
   overall best weight:    2.4202

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 ASN
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7889  Z= 0.213
  Angle     :  0.688   7.284  10670  Z= 0.346
  Chirality :  0.041   0.180   1278
  Planarity :  0.004   0.053   1309
  Dihedral  : 11.309  77.209   1142
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 16.21
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.01 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 12.60 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.10 (0.27), residues: 999
  helix:  1.47 (0.22), residues: 567
  sheet: -2.10 (0.50), residues: 87
  loop : -2.18 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 322 
 HIS   0.006   0.001   HIS B 205 
 PHE   0.017   0.002   PHE C  60 
 TYR   0.013   0.002   TYR D  11 
 ARG   0.000   0.000   ARG B 171 

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4159 (tpp) cc_final: 0.3958 (tpp)
REVERT: B   87 ASN cc_start: 0.9558 (t0) cc_final: 0.8656 (t0)
REVERT: B  207 MET cc_start: 0.8897 (mtm) cc_final: 0.8582 (mtm)
REVERT: C   62 THR cc_start: 0.8730 (p) cc_final: 0.8325 (t)
REVERT: D   87 ASN cc_start: 0.9583 (t0) cc_final: 0.9350 (t0)
REVERT: D  207 MET cc_start: 0.7501 (mpp) cc_final: 0.7239 (mpp)
  outliers start: 19
  outliers final: 14
  residues processed: 78
  average time/residue: 0.1619
  time to fit residues: 18.8306
Evaluate side-chains
  69 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue  118 ARG
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  175 ARG
Chi-restraints excluded: chain C residue   55 HIS
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue  124 ARG
Chi-restraints excluded: chain D residue  206 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   chunk 61 optimal weight:    8.9990
   chunk 24 optimal weight:    8.9990
   chunk 90 optimal weight:    7.9990
   chunk 97 optimal weight:    0.9980
   chunk 80 optimal weight:    7.9990
   chunk 89 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0170
   chunk 72 optimal weight:    7.9990
   overall best weight:    3.2024

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

Flipped N/Q/H residues before XYZ refinement:
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7889  Z= 0.244
  Angle     :  0.673   7.468  10670  Z= 0.342
  Chirality :  0.040   0.186   1278
  Planarity :  0.004   0.053   1309
  Dihedral  : 10.505  76.553   1122
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 18.20
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.91 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 18.19 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.09 (0.27), residues: 999
  helix:  1.47 (0.22), residues: 565
  sheet: -2.07 (0.53), residues: 80
  loop : -2.17 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 318 
 HIS   0.005   0.001   HIS D  88 
 PHE   0.046   0.002   PHE D 180 
 TYR   0.014   0.002   TYR D  11 
 ARG   0.000   0.000   ARG D 219 

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 57
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4408 (tpp) cc_final: 0.4170 (tpp)
REVERT: B  109 MET cc_start: 0.7936 (mmm) cc_final: 0.7573 (mmm)
REVERT: B  207 MET cc_start: 0.8910 (mtm) cc_final: 0.8587 (mtm)
REVERT: C  258 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8530 (ppp)
REVERT: D  109 MET cc_start: 0.8507 (mmt) cc_final: 0.8192 (mmm)
REVERT: D  160 LEU cc_start: 0.9776 (mt) cc_final: 0.9404 (tt)
REVERT: D  180 PHE cc_start: 0.9803 (m-80) cc_final: 0.9587 (m-80)
  outliers start: 21
  outliers final: 18
  residues processed: 74
  average time/residue: 0.1534
  time to fit residues: 17.3798
Evaluate side-chains
  73 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 54
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue  118 ARG
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  175 ARG
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue   55 HIS
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain D residue  124 ARG
Chi-restraints excluded: chain D residue  203 MET
Chi-restraints excluded: chain D residue  206 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 9 optimal weight:   20.0000
   chunk 42 optimal weight:    6.9990
   chunk 60 optimal weight:   40.0000
   chunk 90 optimal weight:    8.9990
   chunk 95 optimal weight:    8.9990
   chunk 47 optimal weight:    9.9990
   chunk 85 optimal weight:   10.0000
   chunk 25 optimal weight:    0.1980
   overall best weight:    2.9986

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

Flipped N/Q/H residues before XYZ refinement:
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 ASN
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7889  Z= 0.224
  Angle     :  0.668   9.075  10670  Z= 0.336
  Chirality :  0.040   0.181   1278
  Planarity :  0.004   0.052   1309
  Dihedral  :  9.909  69.933   1114
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 17.63
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.51 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 19.74 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.05 (0.27), residues: 999
  helix:  1.51 (0.22), residues: 569
  sheet: -2.09 (0.52), residues: 87
  loop : -2.17 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 318 
 HIS   0.004   0.001   HIS D  88 
 PHE   0.023   0.002   PHE D 180 
 TYR   0.014   0.001   TYR D  11 
 ARG   0.000   0.000   ARG B 202 

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 57
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4653 (tpp) cc_final: 0.4412 (tpp)
REVERT: B  207 MET cc_start: 0.8918 (mtm) cc_final: 0.8603 (mtm)
REVERT: C  258 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8453 (ppp)
REVERT: D  180 PHE cc_start: 0.9803 (m-80) cc_final: 0.9544 (m-80)
REVERT: D  207 MET cc_start: 0.7330 (mpp) cc_final: 0.6770 (mpp)
  outliers start: 30
  outliers final: 22
  residues processed: 82
  average time/residue: 0.1433
  time to fit residues: 18.0093
Evaluate side-chains
  78 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 55
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  175 ARG
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain B residue   86 GLN
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue   55 HIS
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain D residue  124 ARG
Chi-restraints excluded: chain D residue  203 MET
Chi-restraints excluded: chain D residue  206 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 79 optimal weight:   20.0000
   chunk 54 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 71 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 85 optimal weight:    9.9990
   chunk 24 optimal weight:    7.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 176 GLN
** D  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7889  Z= 0.165
  Angle     :  0.659   9.342  10670  Z= 0.324
  Chirality :  0.039   0.180   1278
  Planarity :  0.004   0.051   1309
  Dihedral  :  9.506  64.756   1110
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 14.93
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.41 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 22.83 %
    Favored  : 73.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.17 (0.28), residues: 999
  helix:  1.63 (0.23), residues: 567
  sheet: -2.01 (0.52), residues: 87
  loop : -1.95 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 318 
 HIS   0.004   0.001   HIS B 154 
 PHE   0.020   0.002   PHE C  60 
 TYR   0.014   0.001   TYR D  11 
 ARG   0.000   0.000   ARG D 219 

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 59
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8807 (pp20)
REVERT: A  273 LEU cc_start: 0.9668 (tp) cc_final: 0.9274 (pp)
REVERT: B    1 MET cc_start: 0.4429 (tpp) cc_final: 0.4199 (tpp)
REVERT: B  109 MET cc_start: 0.8265 (mmm) cc_final: 0.7908 (mmm)
REVERT: B  207 MET cc_start: 0.8904 (mtm) cc_final: 0.8611 (mtm)
REVERT: D  109 MET cc_start: 0.8470 (mmt) cc_final: 0.8012 (mmm)
REVERT: D  160 LEU cc_start: 0.9736 (mt) cc_final: 0.9347 (tt)
REVERT: D  180 PHE cc_start: 0.9803 (m-80) cc_final: 0.9552 (m-80)
REVERT: D  207 MET cc_start: 0.7358 (mpp) cc_final: 0.7017 (mpp)
  outliers start: 30
  outliers final: 23
  residues processed: 81
  average time/residue: 0.1434
  time to fit residues: 17.9987
Evaluate side-chains
  81 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 57
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue   55 HIS
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue  124 ARG
Chi-restraints excluded: chain D residue  177 MET
Chi-restraints excluded: chain D residue  203 MET
Chi-restraints excluded: chain D residue  206 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 86 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 56 optimal weight:   30.0000
   chunk 23 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   chunk 44 optimal weight:    0.0370
   chunk 7 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   chunk 50 optimal weight:    7.9990
   overall best weight:    3.0064

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

Flipped N/Q/H residues before XYZ refinement:
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7889  Z= 0.226
  Angle     :  0.673   8.078  10670  Z= 0.336
  Chirality :  0.040   0.371   1278
  Planarity :  0.004   0.050   1309
  Dihedral  :  9.272  70.473   1106
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 18.14
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.21 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 22.35 %
    Favored  : 73.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.13 (0.28), residues: 999
  helix:  1.61 (0.22), residues: 571
  sheet: -2.09 (0.53), residues: 80
  loop : -2.04 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 318 
 HIS   0.004   0.001   HIS D  88 
 PHE   0.016   0.001   PHE C  60 
 TYR   0.013   0.001   TYR D  11 
 ARG   0.000   0.000   ARG B 171 

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 55
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.8997 (pm20)
REVERT: A  273 LEU cc_start: 0.9674 (tp) cc_final: 0.9270 (pp)
REVERT: B    1 MET cc_start: 0.4712 (tpp) cc_final: 0.4475 (tpp)
REVERT: B  109 MET cc_start: 0.8284 (mmm) cc_final: 0.7972 (mmm)
REVERT: B  207 MET cc_start: 0.8908 (mtm) cc_final: 0.8569 (mtm)
REVERT: D  109 MET cc_start: 0.8629 (mmt) cc_final: 0.8346 (mmm)
REVERT: D  160 LEU cc_start: 0.9744 (mt) cc_final: 0.9363 (tt)
REVERT: D  180 PHE cc_start: 0.9808 (m-80) cc_final: 0.9561 (m-80)
REVERT: D  207 MET cc_start: 0.7378 (mpp) cc_final: 0.7048 (mpp)
  outliers start: 34
  outliers final: 26
  residues processed: 83
  average time/residue: 0.1452
  time to fit residues: 18.5630
Evaluate side-chains
  82 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 55
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue   55 HIS
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain C residue  118 ARG
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue  124 ARG
Chi-restraints excluded: chain D residue  203 MET
Chi-restraints excluded: chain D residue  206 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 80 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 95 optimal weight:    4.9990
   chunk 59 optimal weight:   20.0000
   chunk 58 optimal weight:    0.1980
   chunk 44 optimal weight:    3.9990
   chunk 38 optimal weight:    9.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7889  Z= 0.170
  Angle     :  0.667  11.227  10670  Z= 0.326
  Chirality :  0.040   0.305   1278
  Planarity :  0.004   0.051   1309
  Dihedral  :  8.946  67.930   1106
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.71 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 23.66 %
    Favored  : 72.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.24 (0.28), residues: 999
  helix:  1.68 (0.22), residues: 574
  sheet: -2.05 (0.53), residues: 80
  loop : -1.98 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 318 
 HIS   0.004   0.001   HIS B 154 
 PHE   0.020   0.001   PHE C  60 
 TYR   0.013   0.001   TYR D  11 
 ARG   0.000   0.000   ARG B 171 

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 59
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8695 (pp20)
REVERT: A  239 GLU cc_start: 0.9386 (OUTLIER) cc_final: 0.8978 (pm20)
REVERT: A  273 LEU cc_start: 0.9683 (tp) cc_final: 0.9290 (pp)
REVERT: B    1 MET cc_start: 0.4503 (tpp) cc_final: 0.4284 (tpp)
REVERT: B  109 MET cc_start: 0.8286 (mmm) cc_final: 0.8003 (mmm)
REVERT: B  207 MET cc_start: 0.8901 (mtm) cc_final: 0.8564 (mtm)
REVERT: C   74 MET cc_start: 0.9035 (mmm) cc_final: 0.8750 (mmm)
REVERT: D  160 LEU cc_start: 0.9738 (mt) cc_final: 0.9371 (tt)
REVERT: D  180 PHE cc_start: 0.9805 (m-80) cc_final: 0.9549 (m-80)
REVERT: D  207 MET cc_start: 0.7444 (mpp) cc_final: 0.7145 (mpp)
  outliers start: 30
  outliers final: 24
  residues processed: 83
  average time/residue: 0.1409
  time to fit residues: 18.0009
Evaluate side-chains
  82 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 56
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  175 GLU
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue   55 HIS
Chi-restraints excluded: chain C residue  118 ARG
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue  203 MET
Chi-restraints excluded: chain D residue  206 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 56 optimal weight:   40.0000
   chunk 28 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   chunk 60 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 75 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 225 ASN
B  99 ASN
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 144 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7889  Z= 0.234
  Angle     :  0.689   9.781  10670  Z= 0.344
  Chirality :  0.041   0.241   1278
  Planarity :  0.004   0.049   1309
  Dihedral  :  8.845  72.480   1098
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 18.01
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.21 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 24.61 %
    Favored  : 72.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.20 (0.27), residues: 999
  helix:  1.63 (0.22), residues: 569
  sheet: -1.73 (0.61), residues: 62
  loop : -2.01 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 318 
 HIS   0.004   0.001   HIS D  88 
 PHE   0.017   0.001   PHE C  60 
 TYR   0.013   0.001   TYR D  11 
 ARG   0.000   0.000   ARG B 185 

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 53
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8757 (pp20)
REVERT: A  273 LEU cc_start: 0.9683 (tp) cc_final: 0.9293 (pp)
REVERT: B    1 MET cc_start: 0.4706 (tpp) cc_final: 0.4484 (tpp)
REVERT: B  109 MET cc_start: 0.8245 (mmm) cc_final: 0.7966 (mmm)
REVERT: B  207 MET cc_start: 0.8897 (mtm) cc_final: 0.8550 (mtm)
REVERT: D   45 LEU cc_start: 0.9723 (pp) cc_final: 0.9483 (pt)
REVERT: D  109 MET cc_start: 0.8774 (mmt) cc_final: 0.8300 (mmm)
REVERT: D  160 LEU cc_start: 0.9766 (mt) cc_final: 0.9370 (tt)
REVERT: D  180 PHE cc_start: 0.9805 (m-80) cc_final: 0.9581 (m-80)
REVERT: D  207 MET cc_start: 0.7463 (mpp) cc_final: 0.7169 (mpp)
  outliers start: 26
  outliers final: 22
  residues processed: 77
  average time/residue: 0.1475
  time to fit residues: 17.5252
Evaluate side-chains
  76 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 53
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue   55 HIS
Chi-restraints excluded: chain C residue  118 ARG
Chi-restraints excluded: chain C residue  203 LEU
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue  203 MET
Chi-restraints excluded: chain D residue  206 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 80 optimal weight:    9.9990
   chunk 84 optimal weight:    2.9990
   chunk 58 optimal weight:   20.0000
   chunk 94 optimal weight:    0.9980
   chunk 57 optimal weight:   20.0000
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7889  Z= 0.188
  Angle     :  0.687   9.898  10670  Z= 0.339
  Chirality :  0.040   0.239   1278
  Planarity :  0.004   0.049   1309
  Dihedral  :  8.571  71.000   1094
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 16.35
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.71 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 24.38 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.24 (0.27), residues: 999
  helix:  1.62 (0.22), residues: 573
  sheet: -1.68 (0.62), residues: 62
  loop : -1.96 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 318 
 HIS   0.004   0.001   HIS B 154 
 PHE   0.017   0.001   PHE C  60 
 TYR   0.013   0.001   TYR D  11 
 ARG   0.000   0.000   ARG D 185 

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 55
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8724 (pp20)
REVERT: A  239 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.9004 (pm20)
REVERT: A  273 LEU cc_start: 0.9687 (tp) cc_final: 0.9290 (pp)
REVERT: B  109 MET cc_start: 0.8225 (mmm) cc_final: 0.7936 (mmm)
REVERT: B  207 MET cc_start: 0.8894 (mtm) cc_final: 0.8546 (mtm)
REVERT: C   74 MET cc_start: 0.9067 (mmm) cc_final: 0.8830 (mmm)
REVERT: D  109 MET cc_start: 0.8758 (mmt) cc_final: 0.8296 (mmm)
REVERT: D  180 PHE cc_start: 0.9807 (m-80) cc_final: 0.9577 (m-80)
REVERT: D  207 MET cc_start: 0.7408 (mpp) cc_final: 0.7142 (mpp)
  outliers start: 26
  outliers final: 21
  residues processed: 77
  average time/residue: 0.1461
  time to fit residues: 17.3320
Evaluate side-chains
  77 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 54
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue   55 HIS
Chi-restraints excluded: chain C residue  118 ARG
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue  203 MET
Chi-restraints excluded: chain D residue  206 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 44 optimal weight:    0.0970
   chunk 65 optimal weight:    6.9990
   chunk 98 optimal weight:    5.9990
   chunk 90 optimal weight:    0.6980
   chunk 78 optimal weight:    7.9990
   chunk 8 optimal weight:    7.9990
   chunk 60 optimal weight:   50.0000
   chunk 48 optimal weight:    8.9990
   chunk 62 optimal weight:    9.9990
   chunk 83 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   overall best weight:    4.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7889  Z= 0.294
  Angle     :  0.753   9.568  10670  Z= 0.377
  Chirality :  0.042   0.233   1278
  Planarity :  0.004   0.046   1309
  Dihedral  :  8.891  80.020   1094
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 21.34
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.81 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 24.73 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.02 (0.27), residues: 999
  helix:  1.42 (0.22), residues: 569
  sheet: -1.81 (0.59), residues: 69
  loop : -2.04 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 318 
 HIS   0.007   0.001   HIS D  88 
 PHE   0.016   0.002   PHE C  60 
 TYR   0.015   0.001   TYR D  11 
 ARG   0.000   0.000   ARG B 171 

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 55
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8828 (pp20)
REVERT: A  273 LEU cc_start: 0.9720 (tp) cc_final: 0.9362 (pp)
REVERT: B    1 MET cc_start: 0.4716 (tpp) cc_final: 0.4411 (tpp)
REVERT: B  207 MET cc_start: 0.8889 (mtm) cc_final: 0.8409 (mtm)
REVERT: D  109 MET cc_start: 0.8802 (mmt) cc_final: 0.8354 (mmm)
REVERT: D  180 PHE cc_start: 0.9808 (m-80) cc_final: 0.9561 (m-80)
REVERT: D  207 MET cc_start: 0.7500 (mpp) cc_final: 0.7264 (mpp)
  outliers start: 22
  outliers final: 20
  residues processed: 76
  average time/residue: 0.1433
  time to fit residues: 16.8237
Evaluate side-chains
  76 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 55
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue   55 HIS
Chi-restraints excluded: chain C residue  118 ARG
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue  206 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 11 optimal weight:   50.0000
   chunk 21 optimal weight:   10.0000
   chunk 78 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 80 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   chunk 69 optimal weight:    0.3980
   chunk 4 optimal weight:    5.9990
   chunk 56 optimal weight:   20.0000
   overall best weight:    4.0788

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

Flipped N/Q/H residues before XYZ refinement:
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  86 GLN ** 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 = 0.3129 r_free = 0.3129 target = 0.042008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.029981 restraints weight = 70592.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.030645 restraints weight = 50064.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.031125 restraints weight = 39127.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7889  Z= 0.274
  Angle     :  0.751  10.255  10670  Z= 0.370
  Chirality :  0.042   0.225   1278
  Planarity :  0.004   0.047   1309
  Dihedral  :  8.886  81.472   1094
  Min Nonbonded Distance : 1.846

Molprobity Statistics.
  All-atom Clashscore : 19.42
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.11 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 24.85 %
    Favored  : 72.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.04 (0.27), residues: 999
  helix:  1.37 (0.22), residues: 570
  sheet: -1.87 (0.57), residues: 69
  loop : -1.97 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 318 
 HIS   0.006   0.001   HIS D  88 
 PHE   0.021   0.002   PHE C  60 
 TYR   0.014   0.001   TYR D  11 
 ARG   0.000   0.000   ARG D 206 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1565.41 seconds
wall clock time: 29 minutes 16.57 seconds (1756.57 seconds total)