Starting phenix.real_space_refine
on Fri Dec  8 10:43:04 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/12_2023/7wf7_32461_neut_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/12_2023/7wf7_32461.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/12_2023/7wf7_32461_neut_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/12_2023/7wf7_32461_neut_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/12_2023/7wf7_32461_neut_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/12_2023/7wf7_32461.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/12_2023/7wf7_32461.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/12_2023/7wf7_32461_neut_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/12_2023/7wf7_32461_neut_updated.pdb"
  }
  resolution = 3.4
  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=  -0.003 sd=   0.113
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      56      5.16       5
     C    5207      2.51       5
     N    1380      2.21       5
     O    1492      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "C PHE  151": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  216": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8136
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2189
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 6, 'TRANS': 264}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 1143
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 1143
          Classifications: {'peptide': 142}
          Link IDs: {'TRANS': 141}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 2592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2592
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
    Chain: "D"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 410
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
    Chain: "E"
      Number of atoms: 1777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1777
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'S1P': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.56, per 1000 atoms: 0.56
  Number of scatterers: 8136
  At special positions: 0
  Unit cell: (92.4, 124.3, 132, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      56     16.00
     P       1     15.00
     O    1492      8.00
     N    1380      7.00
     C    5207      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 184 " - pdb=" SG  CYS A 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.05

  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=0, symmetry=0
  Time building additional restraints: 2.98
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1932

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      24 helices and 13 sheets defined
      31.4% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 32
    Processing helix  chain 'A' and resid 47 through 71
    Processing helix  chain 'A' and resid 79 through 103
    Processing helix  chain 'A' and resid 107 through 110
    Processing helix  chain 'A' and resid 114 through 145
    Processing helix  chain 'A' and resid 159 through 180
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 188 through 190
      No H-bonds generated for 'chain 'A' and resid 188 through 190'
    Processing helix  chain 'A' and resid 202 through 233
    Processing helix  chain 'A' and resid 255 through 279
      removed outlier: 5.200A  pdb=" N   ILE A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   PHE A 265 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
      Proline residue:  A 271  - end of helix
      removed outlier: 3.757A  pdb=" N   LEU A 277 " --> pdb=" O   PHE A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 291
    Processing helix  chain 'A' and resid 297 through 305
      removed outlier: 4.134A  pdb=" N   SER A 304 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   GLY A 305 " --> pdb=" O   VAL A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 310
      No H-bonds generated for 'chain 'A' and resid 307 through 310'
    Processing helix  chain 'A' and resid 316 through 323
    Processing helix  chain 'B' and resid 7 through 32
      removed outlier: 4.009A  pdb=" N   ALA B  11 " --> pdb=" O   ALA B   7 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   ARG B  32 " --> pdb=" O   GLU B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 52
      removed outlier: 4.008A  pdb=" N   LYS B  51 " --> pdb=" O   SER B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 216
      removed outlier: 3.822A  pdb=" N   GLU B 216 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 350
      removed outlier: 4.588A  pdb=" N   PHE B 334 " --> pdb=" O   ASN B 331 " (cutoff:3.500A)
      removed outlier: 5.110A  pdb=" N   LYS B 345 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 5 through 23
    Processing helix  chain 'C' and resid 30 through 36
      removed outlier: 5.090A  pdb=" N   ASN C  35 " --> pdb=" O   SER C  31 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   ASN C  36 " --> pdb=" O   GLN C  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 11 through 23
    Processing helix  chain 'D' and resid 30 through 43
    Processing helix  chain 'D' and resid 56 through 58
      No H-bonds generated for 'chain 'D' and resid 56 through 58'
    Processing helix  chain 'E' and resid 29 through 31
      No H-bonds generated for 'chain 'E' and resid 29 through 31'
    Processing helix  chain 'E' and resid 88 through 90
      No H-bonds generated for 'chain 'E' and resid 88 through 90'
    Processing sheet with id=  A, first strand: chain 'B' and resid 264 through 266
      removed outlier: 6.264A  pdb=" N   ILE B 221 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'C' and resid 58 through 63
      removed outlier: 6.936A  pdb=" N   ALA C  73 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   MET C  61 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  61 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   TRP C  63 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   LEU C  69 " --> pdb=" O   TRP C  63 " (cutoff:3.500A)
      removed outlier: 5.982A  pdb=" N   ASP C  83 " --> pdb=" O   LYS C  89 " (cutoff:3.500A)
      removed outlier: 5.335A  pdb=" N   LYS C  89 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'C' and resid 100 through 105
      removed outlier: 7.162A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   GLY C 116 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
      removed outlier: 5.151A  pdb=" N   ILE C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'C' and resid 146 through 151
      removed outlier: 6.838A  pdb=" N   SER C 160 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   CYS C 149 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   VAL C 158 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   PHE C 151 " --> pdb=" O   GLN C 156 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   GLN C 156 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'C' and resid 220 through 223
      removed outlier: 4.283A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   SER C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL C 200 " --> pdb=" O   SER C 191 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   SER C 189 " --> pdb=" O   GLY C 202 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.573A  pdb=" N   GLY C 244 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ILE C 232 " --> pdb=" O   ALA C 242 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   ALA C 242 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 4.957A  pdb=" N   PHE C 234 " --> pdb=" O   ALA C 240 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   ALA C 240 " --> pdb=" O   PHE C 234 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   THR C 249 " --> pdb=" O   SER C 245 " (cutoff:3.500A)
      removed outlier: 5.662A  pdb=" N   ASP C 254 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 5.394A  pdb=" N   GLU C 260 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'C' and resid 305 through 307
      removed outlier: 4.009A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'C' and resid 47 through 51
      removed outlier: 7.090A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.878A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=  J, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.316A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   ALA E  40 " --> pdb=" O   LEU E  45 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   LEU E  45 " --> pdb=" O   ALA E  40 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'E' and resid 128 through 130
    Processing sheet with id=  L, first strand: chain 'E' and resid 134 through 136
      removed outlier: 7.228A  pdb=" N   LYS E 232 " --> pdb=" O   VAL E 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  L
    Processing sheet with id=  M, first strand: chain 'E' and resid 213 through 219
      removed outlier: 6.291A  pdb=" N   LEU E 166 " --> pdb=" O   LEU E 175 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   LEU E 175 " --> pdb=" O   LEU E 166 " (cutoff:3.500A)

    361 hydrogen bonds defined for protein.
    981 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: 2.47

  Time building geometry restraints manager: 3.21 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: 2565
        1.34 -     1.46: 1956
        1.46 -     1.58: 3686
        1.58 -     1.70: 6
        1.70 -     1.83: 81
  Bond restraints: 8294
  Sorted by residual:
  bond pdb=" O1  S1P A 401 "
       pdb=" P22 S1P A 401 "
    ideal  model  delta    sigma   weight residual
    1.661  1.815 -0.154 2.00e-02 2.50e+03 5.94e+01
  bond pdb=" C5  S1P A 401 "
       pdb=" C6  S1P A 401 "
    ideal  model  delta    sigma   weight residual
    1.550  1.486  0.064 2.00e-02 2.50e+03 1.02e+01
  bond pdb=" C13 S1P A 401 "
       pdb=" C14 S1P A 401 "
    ideal  model  delta    sigma   weight residual
    1.569  1.509  0.060 2.00e-02 2.50e+03 9.11e+00
  bond pdb=" C6  S1P A 401 "
       pdb=" C7  S1P A 401 "
    ideal  model  delta    sigma   weight residual
    1.554  1.606 -0.052 2.00e-02 2.50e+03 6.84e+00
  bond pdb=" C15 S1P A 401 "
       pdb=" C16 S1P A 401 "
    ideal  model  delta    sigma   weight residual
    1.561  1.510  0.051 2.00e-02 2.50e+03 6.61e+00
  ... (remaining 8289 not shown)

  Histogram of bond angle deviations from ideal:
       95.09 -   102.88: 40
      102.88 -   110.67: 2514
      110.67 -   118.46: 3901
      118.46 -   126.25: 4634
      126.25 -   134.04: 128
  Bond angle restraints: 11217
  Sorted by residual:
  angle pdb=" O1  S1P A 401 "
        pdb=" P22 S1P A 401 "
        pdb=" O25 S1P A 401 "
      ideal   model   delta    sigma   weight residual
     109.48   95.09   14.39 3.00e+00 1.11e-01 2.30e+01
  angle pdb=" N   PHE C 235 "
        pdb=" CA  PHE C 235 "
        pdb=" C   PHE C 235 "
      ideal   model   delta    sigma   weight residual
     108.85  100.57    8.28 1.88e+00 2.83e-01 1.94e+01
  angle pdb=" N   TYR E  94 "
        pdb=" CA  TYR E  94 "
        pdb=" C   TYR E  94 "
      ideal   model   delta    sigma   weight residual
     108.76  115.88   -7.12 1.69e+00 3.50e-01 1.78e+01
  angle pdb=" C   PHE C 235 "
        pdb=" CA  PHE C 235 "
        pdb=" CB  PHE C 235 "
      ideal   model   delta    sigma   weight residual
     110.13  115.24   -5.11 1.34e+00 5.57e-01 1.46e+01
  angle pdb=" C   LEU C  70 "
        pdb=" CA  LEU C  70 "
        pdb=" CB  LEU C  70 "
      ideal   model   delta    sigma   weight residual
     109.65  103.02    6.63 1.75e+00 3.27e-01 1.44e+01
  ... (remaining 11212 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.76: 4716
       26.76 -    53.52: 170
       53.52 -    80.28: 12
       80.28 -   107.04: 4
      107.04 -   133.80: 2
  Dihedral angle restraints: 4904
    sinusoidal: 1917
      harmonic: 2987
  Sorted by residual:
  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  133.38  -40.38     1      1.00e+01 1.00e-02 2.29e+01
  dihedral pdb=" C10 S1P A 401 "
           pdb=" C11 S1P A 401 "
           pdb=" C12 S1P A 401 "
           pdb=" C13 S1P A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     222.74   88.94  133.80     1      3.00e+01 1.11e-03 1.80e+01
  dihedral pdb=" CA  ASN C 293 "
           pdb=" C   ASN C 293 "
           pdb=" N   CYS C 294 "
           pdb=" CA  CYS C 294 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.02   19.98     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 4901 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 942
       0.045 -    0.090: 263
       0.090 -    0.136: 83
       0.136 -    0.181: 6
       0.181 -    0.226: 4
  Chirality restraints: 1298
  Sorted by residual:
  chirality pdb=" CA  ASP C 247 "
            pdb=" N   ASP C 247 "
            pdb=" C   ASP C 247 "
            pdb=" CB  ASP C 247 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" C3  S1P A 401 "
            pdb=" C2  S1P A 401 "
            pdb=" C4  S1P A 401 "
            pdb=" O3  S1P A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52   -2.32   -0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  LYS A 256 "
            pdb=" N   LYS A 256 "
            pdb=" C   LYS A 256 "
            pdb=" CB  LYS A 256 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1295 not shown)

  Planarity restraints: 1388
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 169 "   -0.026 2.00e-02 2.50e+03   1.89e-02 8.94e+00
        pdb=" CG  TRP C 169 "    0.050 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 169 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 169 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 169 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 169 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 169 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 169 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 169 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 169 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E 106 "   -0.042 5.00e-02 4.00e+02   6.51e-02 6.77e+00
        pdb=" N   PRO E 107 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO E 107 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO E 107 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 307 "    0.034 5.00e-02 4.00e+02   5.20e-02 4.32e+00
        pdb=" N   PRO A 308 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 308 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 308 "    0.029 5.00e-02 4.00e+02
  ... (remaining 1385 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2248
        2.81 -     3.33: 7374
        3.33 -     3.86: 12724
        3.86 -     4.38: 14790
        4.38 -     4.90: 25716
  Nonbonded interactions: 62852
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 143 "
            pdb=" OD1 ASP C 163 "
     model   vdw
     2.288 2.440
  nonbonded pdb=" N   GLY C 144 "
            pdb=" OD1 ASP C 163 "
     model   vdw
     2.295 2.520
  nonbonded pdb=" O   ARG C 314 "
            pdb=" OG  SER C 331 "
     model   vdw
     2.297 2.440
  nonbonded pdb=" OG1 THR C  34 "
            pdb=" O   LEU C 300 "
     model   vdw
     2.320 2.440
  nonbonded pdb=" O   SER E 120 "
            pdb=" OG  SER E 120 "
     model   vdw
     2.328 2.440
  ... (remaining 62847 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             0.790
  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:          3.940
  Check model and map are aligned:         0.130
  Set scattering table:                    0.080
  Process input model:                     24.370
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  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:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6250
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.154   8294  Z= 0.265
  Angle     :  0.835  14.386  11217  Z= 0.459
  Chirality :  0.046   0.226   1298
  Planarity :  0.005   0.065   1388
  Dihedral  : 13.778 133.800   2966
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -1.14 (0.26), residues: 1002
  helix:  0.94 (0.30), residues: 297
  sheet: -0.65 (0.30), residues: 266
  loop : -2.04 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.050   0.003   TRP C 169 
   HIS   0.008   0.001   HIS C  91 
   PHE   0.017   0.002   PHE C 151 
   TYR   0.023   0.002   TYR A 198 
   ARG   0.019   0.001   ARG E  98 

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.2155
  time to fit residues: 43.7856
Evaluate side-chains
  100 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.806 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2938
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 77 optimal weight:    9.9990
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 41 optimal weight:    6.9990
   chunk 79 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  36 ASN
A 101 ASN
B 347 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6388
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8294  Z= 0.233
  Angle     :  0.664   8.950  11217  Z= 0.350
  Chirality :  0.044   0.166   1298
  Planarity :  0.005   0.050   1388
  Dihedral  :  7.797 120.487   1128
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  9.00 %
    Favored  : 89.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.71 (0.26), residues: 1002
  helix:  1.57 (0.30), residues: 296
  sheet: -0.48 (0.30), residues: 259
  loop : -1.92 (0.28), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.033   0.002   TRP C 169 
   HIS   0.008   0.001   HIS E 220 
   PHE   0.023   0.002   PHE C 234 
   TYR   0.021   0.002   TYR C 105 
   ARG   0.006   0.000   ARG E  98 

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.957 
Fit side-chains
  outliers start: 12
  outliers final: 7
  residues processed: 108
  average time/residue: 0.2437
  time to fit residues: 34.8544
Evaluate side-chains
  104 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.840 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0819
  time to fit residues: 2.2843
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 77 optimal weight:    0.2980
   chunk 63 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 92 optimal weight:    0.0770
   chunk 100 optimal weight:    0.7980
   chunk 82 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 74 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    0.5538

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6327
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8294  Z= 0.151
  Angle     :  0.567   7.260  11217  Z= 0.300
  Chirality :  0.041   0.155   1298
  Planarity :  0.004   0.042   1388
  Dihedral  :  6.981 111.591   1128
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 11.14 %
    Favored  : 87.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.35 (0.26), residues: 1002
  helix:  2.00 (0.30), residues: 296
  sheet: -0.35 (0.30), residues: 250
  loop : -1.73 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.021   0.002   TRP C 169 
   HIS   0.005   0.001   HIS E 220 
   PHE   0.021   0.001   PHE A 291 
   TYR   0.016   0.001   TYR A 198 
   ARG   0.003   0.000   ARG E  98 

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.843 
Fit side-chains
  outliers start: 10
  outliers final: 4
  residues processed: 116
  average time/residue: 0.2192
  time to fit residues: 34.4780
Evaluate side-chains
  109 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.994 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0738
  time to fit residues: 1.8603
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 93 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** E  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6420
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8294  Z= 0.223
  Angle     :  0.623   9.631  11217  Z= 0.329
  Chirality :  0.043   0.160   1298
  Planarity :  0.004   0.040   1388
  Dihedral  :  6.814 102.091   1128
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 12.37 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 (0.26), residues: 1002
  helix:  1.94 (0.30), residues: 297
  sheet: -0.48 (0.30), residues: 244
  loop : -1.73 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.024   0.002   TRP C 169 
   HIS   0.007   0.001   HIS E 220 
   PHE   0.021   0.002   PHE C 234 
   TYR   0.018   0.002   TYR C 105 
   ARG   0.005   0.000   ARG E  98 

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.920 
Fit side-chains
  outliers start: 21
  outliers final: 10
  residues processed: 121
  average time/residue: 0.2260
  time to fit residues: 36.6520
Evaluate side-chains
  100 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.899 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0736
  time to fit residues: 2.6296
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0070
   chunk 84 optimal weight:    0.0870
   chunk 68 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 50 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 19 optimal weight:    0.3980
   overall best weight:    0.4776

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

Flipped N/Q/H residues before XYZ refinement:
** E  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6330
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8294  Z= 0.143
  Angle     :  0.552   8.835  11217  Z= 0.289
  Chirality :  0.041   0.148   1298
  Planarity :  0.004   0.039   1388
  Dihedral  :  6.269  86.815   1128
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.72 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: 1002
  helix:  2.21 (0.31), residues: 296
  sheet: -0.13 (0.31), residues: 243
  loop : -1.52 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.021   0.001   TRP C  82 
   HIS   0.003   0.001   HIS E 220 
   PHE   0.013   0.001   PHE A 291 
   TYR   0.014   0.001   TYR A 198 
   ARG   0.002   0.000   ARG E  98 

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.889 
Fit side-chains
  outliers start: 14
  outliers final: 11
  residues processed: 113
  average time/residue: 0.2003
  time to fit residues: 31.3730
Evaluate side-chains
  109 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.898 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0807
  time to fit residues: 2.8629
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 98 optimal weight:    0.0770
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 8 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.1742

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6431
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8294  Z= 0.231
  Angle     :  0.626   7.635  11217  Z= 0.329
  Chirality :  0.042   0.153   1298
  Planarity :  0.004   0.038   1388
  Dihedral  :  6.355  81.596   1128
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 15.30 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.23 (0.26), residues: 1002
  helix:  2.14 (0.30), residues: 294
  sheet: -0.38 (0.31), residues: 244
  loop : -1.59 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.023   0.002   TRP C 169 
   HIS   0.008   0.001   HIS E 220 
   PHE   0.020   0.001   PHE C 234 
   TYR   0.016   0.002   TYR C 105 
   ARG   0.004   0.000   ARG E  98 

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.821 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 98
  average time/residue: 0.2094
  time to fit residues: 28.0501
Evaluate side-chains
  95 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.815 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0731
  time to fit residues: 1.6777
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 98 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 60 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6389
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8294  Z= 0.175
  Angle     :  0.576   7.329  11217  Z= 0.303
  Chirality :  0.041   0.147   1298
  Planarity :  0.004   0.038   1388
  Dihedral  :  6.118  72.282   1128
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 16.09 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.06 (0.27), residues: 1002
  helix:  2.26 (0.31), residues: 294
  sheet: -0.27 (0.31), residues: 243
  loop : -1.47 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.002   TRP C  82 
   HIS   0.005   0.001   HIS E 220 
   PHE   0.015   0.001   PHE C 234 
   TYR   0.013   0.001   TYR A 198 
   ARG   0.002   0.000   ARG C 197 

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.869 
Fit side-chains
  outliers start: 9
  outliers final: 3
  residues processed: 102
  average time/residue: 0.2218
  time to fit residues: 30.8134
Evaluate side-chains
  94 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 0.884 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0792
  time to fit residues: 1.7350
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 9 optimal weight:    9.9990
   chunk 77 optimal weight:   10.0000
   chunk 89 optimal weight:    0.1980
   chunk 94 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.7384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6382
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8294  Z= 0.173
  Angle     :  0.573   7.200  11217  Z= 0.300
  Chirality :  0.041   0.146   1298
  Planarity :  0.004   0.038   1388
  Dihedral  :  5.966  63.690   1128
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 16.65 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.00 (0.27), residues: 1002
  helix:  2.31 (0.31), residues: 294
  sheet: -0.29 (0.31), residues: 243
  loop : -1.41 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.002   TRP C  82 
   HIS   0.004   0.001   HIS E 220 
   PHE   0.015   0.001   PHE C 234 
   TYR   0.013   0.001   TYR A 198 
   ARG   0.006   0.000   ARG C 314 

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.957 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 100
  average time/residue: 0.2349
  time to fit residues: 31.6842
Evaluate side-chains
  99 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.943 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0720
  time to fit residues: 1.8375
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 86 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 96 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   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  52 GLN
B 331 ASN
E  82 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6389
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8294  Z= 0.178
  Angle     :  0.582   7.069  11217  Z= 0.304
  Chirality :  0.041   0.148   1298
  Planarity :  0.004   0.040   1388
  Dihedral  :  5.907  56.330   1128
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 16.99 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.01 (0.27), residues: 1002
  helix:  2.31 (0.31), residues: 294
  sheet: -0.32 (0.31), residues: 248
  loop : -1.37 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP C  82 
   HIS   0.004   0.001   HIS E 220 
   PHE   0.016   0.001   PHE C 234 
   TYR   0.013   0.001   TYR A 198 
   ARG   0.003   0.000   ARG C 314 

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 0.914 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 95
  average time/residue: 0.2337
  time to fit residues: 29.9227
Evaluate side-chains
  94 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.887 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0880
  time to fit residues: 1.5678
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9980
   chunk 8 optimal weight:    7.9990
   chunk 62 optimal weight:    0.0030
   chunk 49 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 24 optimal weight:   10.0000
   chunk 74 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0370
   overall best weight:    0.5068

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

Flipped N/Q/H residues before XYZ refinement:
B  52 GLN
** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6343
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8294  Z= 0.145
  Angle     :  0.557   7.068  11217  Z= 0.288
  Chirality :  0.041   0.162   1298
  Planarity :  0.004   0.041   1388
  Dihedral  :  5.715  56.216   1128
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 17.10 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.18 (0.27), residues: 1002
  helix:  2.57 (0.31), residues: 288
  sheet: -0.30 (0.30), residues: 261
  loop : -1.28 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.002   TRP C  82 
   HIS   0.003   0.001   HIS E 220 
   PHE   0.014   0.001   PHE C 234 
   TYR   0.013   0.001   TYR A 198 
   ARG   0.002   0.000   ARG C 314 

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.821 
Fit side-chains
  outliers start: 5
  outliers final: 1
  residues processed: 99
  average time/residue: 0.2117
  time to fit residues: 28.5723
Evaluate side-chains
  94 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.875 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1097
  time to fit residues: 1.4967
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 83 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 71 optimal weight:    4.9990
   chunk 4 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   chunk 92 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    2.9788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.246531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.232915 restraints weight = 9342.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.4443 rms_B_bonded: 0.80
r_work: 0.4350 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.4311 rms_B_bonded: 2.29 restraints_weight: 0.2500
r_work (final): 0.4311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6234
moved from start:          0.3320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.084   8294  Z= 0.496
  Angle     :  0.866  11.648  11217  Z= 0.447
  Chirality :  0.050   0.294   1298
  Planarity :  0.006   0.042   1388
  Dihedral  :  6.716  59.974   1128
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.88 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 17.44 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.59 (0.26), residues: 1002
  helix:  1.70 (0.30), residues: 295
  sheet: -0.57 (0.31), residues: 245
  loop : -1.72 (0.27), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.035   0.003   TRP C 169 
   HIS   0.007   0.002   HIS E  35 
   PHE   0.035   0.003   PHE C 234 
   TYR   0.036   0.003   TYR C 105 
   ARG   0.007   0.001   ARG E  98 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1866.52 seconds
wall clock time: 34 minutes 49.80 seconds (2089.80 seconds total)