Starting phenix.real_space_refine
on Sat Dec 28 13:08:35 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xjj_33229/12_2024/7xjj_33229.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xjj_33229/12_2024/7xjj_33229.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xjj_33229/12_2024/7xjj_33229.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xjj_33229/12_2024/7xjj_33229.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xjj_33229/12_2024/7xjj_33229.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xjj_33229/12_2024/7xjj_33229.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.102
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    5559      2.51       5
     N    1473      2.21       5
     O    1621      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 8710
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1691
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 4, 'TRANS': 210}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 20
    Chain: "B"
      Number of atoms: 2597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2597
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 121
          Classifications: {'peptide': 17}
          Link IDs: {'PTRANS': 1, 'TRANS': 15}
    Chain: "E"
      Number of atoms: 2095
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 2095
          Classifications: {'peptide': 269}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 11, 'TRANS': 257}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 47
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
    Chain: "G"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "S"
      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
  Time building chain proxies: 5.15, per 1000 atoms: 0.59
  Number of scatterers: 8710
  At special positions: 0
  Unit cell: (88.047, 119.57, 125.005, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      57     16.00
     O    1621      8.00
     N    1473      7.00
     C    5559      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 108 " - pdb=" SG  CYS E 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.37
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2102

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 14 sheets defined
      36.9% alpha, 21.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
    Processing helix  chain 'A' and resid 243 through 256
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 3.505A  pdb=" N   PHE A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   LYS A 280 " --> pdb=" O   GLY A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 310
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.955A  pdb=" N   ILE A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'C' and resid 3 through 12
    Processing helix  chain 'C' and resid 12 through 17
    Processing helix  chain 'E' and resid 34 through 59
    Processing helix  chain 'E' and resid 69 through 98
      Proline residue:  E  90  - end of helix
    Processing helix  chain 'E' and resid 103 through 139
      removed outlier: 4.141A  pdb=" N   ILE E 107 " --> pdb=" O   LEU E 103 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 149 through 173
      removed outlier: 3.613A  pdb=" N   ALA E 165 " --> pdb=" O   ALA E 161 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   MET E 166 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      Proline residue:  E 169  - end of helix
    Processing helix  chain 'E' and resid 193 through 231
      removed outlier: 3.714A  pdb=" N   LYS E 197 " --> pdb=" O   ASP E 193 " (cutoff:3.500A)
      Proline residue:  E 212  - end of helix
    Processing helix  chain 'E' and resid 235 through 272
      Proline residue:  E 262  - end of helix
    Processing helix  chain 'E' and resid 278 through 304
      Proline residue:  E 300  - end of helix
    Processing helix  chain 'E' and resid 307 through 317
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.710A  pdb=" N   ALA G  12 " --> pdb=" O   SER G   8 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.625A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 4.083A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188
      removed outlier: 5.915A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 8.355A  pdb=" N   ASP A 227 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52
      removed outlier: 6.612A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.881A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 103
      removed outlier: 6.959A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.869A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.003A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.738A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.713A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.676A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   SER B 277 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ALA B 287 " --> pdb=" O   ASN B 295 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 174 through 177
    Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.689A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 116 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136
      removed outlier: 6.247A  pdb=" N   VAL S 135 " --> pdb=" O   GLU S 234 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 143 through 148

    447 hydrogen bonds defined for protein.
    1272 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: 2.38

  Time building geometry restraints manager: 2.75 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1405
        1.27 -     1.41: 2326
        1.41 -     1.55: 5090
        1.55 -     1.69: 3
        1.69 -     1.83: 80
  Bond restraints: 8904
  Sorted by residual:
  bond pdb=" C   LEU A  23 "
       pdb=" O   LEU A  23 "
    ideal  model  delta    sigma   weight residual
    1.237  1.131  0.106 1.17e-02 7.31e+03 8.14e+01
  bond pdb=" CA  LEU A  23 "
       pdb=" C   LEU A  23 "
    ideal  model  delta    sigma   weight residual
    1.523  1.409  0.114 1.30e-02 5.92e+03 7.68e+01
  bond pdb=" C   ASN A  22 "
       pdb=" O   ASN A  22 "
    ideal  model  delta    sigma   weight residual
    1.237  1.138  0.098 1.16e-02 7.43e+03 7.19e+01
  bond pdb=" CA  ASP A  26 "
       pdb=" C   ASP A  26 "
    ideal  model  delta    sigma   weight residual
    1.524  1.433  0.090 1.29e-02 6.01e+03 4.89e+01
  bond pdb=" C   ASP A  26 "
       pdb=" O   ASP A  26 "
    ideal  model  delta    sigma   weight residual
    1.237  1.155  0.081 1.19e-02 7.06e+03 4.67e+01
  ... (remaining 8899 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.22: 11986
        4.22 -     8.43: 93
        8.43 -    12.65: 7
       12.65 -    16.86: 2
       16.86 -    21.08: 2
  Bond angle restraints: 12090
  Sorted by residual:
  angle pdb=" N   LYS A  35 "
        pdb=" CA  LYS A  35 "
        pdb=" C   LYS A  35 "
      ideal   model   delta    sigma   weight residual
     110.36  131.10  -20.74 1.55e+00 4.16e-01 1.79e+02
  angle pdb=" N   GLY E 157 "
        pdb=" CA  GLY E 157 "
        pdb=" C   GLY E 157 "
      ideal   model   delta    sigma   weight residual
     112.83  101.71   11.12 1.22e+00 6.72e-01 8.31e+01
  angle pdb=" CA  PRO E 169 "
        pdb=" N   PRO E 169 "
        pdb=" CD  PRO E 169 "
      ideal   model   delta    sigma   weight residual
     112.00  101.15   10.85 1.40e+00 5.10e-01 6.00e+01
  angle pdb=" CA  LYS A  32 "
        pdb=" C   LYS A  32 "
        pdb=" N   ASP A  33 "
      ideal   model   delta    sigma   weight residual
     117.30  125.75   -8.45 1.16e+00 7.43e-01 5.31e+01
  angle pdb=" CA  CYS E 158 "
        pdb=" CB  CYS E 158 "
        pdb=" SG  CYS E 158 "
      ideal   model   delta    sigma   weight residual
     114.40   98.13   16.27 2.30e+00 1.89e-01 5.01e+01
  ... (remaining 12085 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 4708
       18.00 -    36.00: 425
       36.00 -    54.00: 72
       54.00 -    72.00: 14
       72.00 -    90.00: 4
  Dihedral angle restraints: 5223
    sinusoidal: 1965
      harmonic: 3258
  Sorted by residual:
  dihedral pdb=" C   MET E 166 "
           pdb=" N   MET E 166 "
           pdb=" CA  MET E 166 "
           pdb=" CB  MET E 166 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -149.39   26.79     0      2.50e+00 1.60e-01 1.15e+02
  dihedral pdb=" N   MET E 166 "
           pdb=" C   MET E 166 "
           pdb=" CA  MET E 166 "
           pdb=" CB  MET E 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  146.38  -23.58     0      2.50e+00 1.60e-01 8.90e+01
  dihedral pdb=" C   ILE A  28 "
           pdb=" N   ILE A  28 "
           pdb=" CA  ILE A  28 "
           pdb=" CB  ILE A  28 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -137.24   15.24     0      2.50e+00 1.60e-01 3.72e+01
  ... (remaining 5220 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.219: 1366
       0.219 -    0.439: 8
       0.439 -    0.658: 3
       0.658 -    0.877: 2
       0.877 -    1.097: 1
  Chirality restraints: 1380
  Sorted by residual:
  chirality pdb=" CA  MET E 166 "
            pdb=" N   MET E 166 "
            pdb=" C   MET E 166 "
            pdb=" CB  MET E 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.41    1.10 2.00e-01 2.50e+01 3.01e+01
  chirality pdb=" CA  PRO E 169 "
            pdb=" N   PRO E 169 "
            pdb=" C   PRO E 169 "
            pdb=" CB  PRO E 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    1.95    0.77 2.00e-01 2.50e+01 1.47e+01
  chirality pdb=" CA  LYS A  35 "
            pdb=" N   LYS A  35 "
            pdb=" C   LYS A  35 "
            pdb=" CB  LYS A  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.85    0.66 2.00e-01 2.50e+01 1.09e+01
  ... (remaining 1377 not shown)

  Planarity restraints: 1531
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E 168 "   -0.157 5.00e-02 4.00e+02   2.38e-01 9.05e+01
        pdb=" N   PRO E 169 "    0.411 5.00e-02 4.00e+02
        pdb=" CA  PRO E 169 "   -0.135 5.00e-02 4.00e+02
        pdb=" CD  PRO E 169 "   -0.119 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E 156 "   -0.025 2.00e-02 2.50e+03   5.16e-02 2.66e+01
        pdb=" C   VAL E 156 "    0.089 2.00e-02 2.50e+03
        pdb=" O   VAL E 156 "   -0.034 2.00e-02 2.50e+03
        pdb=" N   GLY E 157 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E 188 "    0.033 2.00e-02 2.50e+03   3.00e-02 2.24e+01
        pdb=" CG  TRP E 188 "   -0.080 2.00e-02 2.50e+03
        pdb=" CD1 TRP E 188 "    0.038 2.00e-02 2.50e+03
        pdb=" CD2 TRP E 188 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP E 188 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP E 188 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP E 188 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E 188 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E 188 "    0.010 2.00e-02 2.50e+03
        pdb=" CH2 TRP E 188 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1528 not shown)

  Histogram of nonbonded interaction distances:
        1.77 -     2.40: 47
        2.40 -     3.02: 5273
        3.02 -     3.65: 13354
        3.65 -     4.27: 19467
        4.27 -     4.90: 33595
  Nonbonded interactions: 71736
  Sorted by model distance:
  nonbonded pdb=" O   LYS A  35 "
            pdb=" CG  LEU A  36 "
     model   vdw
     1.771 3.470
  nonbonded pdb=" O   LYS A  35 "
            pdb=" CD2 LEU A  36 "
     model   vdw
     1.950 3.460
  nonbonded pdb=" CE1 TYR E 113 "
            pdb=" CB  ALA E 167 "
     model   vdw
     1.990 3.760
  nonbonded pdb=" O   ASN E  33 "
            pdb=" OG1 THR E  36 "
     model   vdw
     2.139 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.149 3.040
  ... (remaining 71731 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.350
  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:             0.300
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     22.320
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  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:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
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      :  0.007   0.114   8904  Z= 0.456
  Angle     :  0.879  21.081  12090  Z= 0.529
  Chirality :  0.070   1.097   1380
  Planarity :  0.008   0.238   1531
  Dihedral  : 14.108  89.998   3115
  Min Nonbonded Distance : 1.771

Molprobity Statistics.
  All-atom Clashscore : 16.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  1.49 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.48 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.40 (0.26), residues: 1104
  helix:  2.09 (0.25), residues: 383
  sheet: -0.58 (0.31), residues: 255
  loop : -0.74 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.080   0.003   TRP E 188 
 HIS   0.006   0.001   HIS E 289 
 PHE   0.018   0.001   PHE E 114 
 TYR   0.017   0.001   TYR S 101 
 ARG   0.008   0.000   ARG B 129 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 173
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8114 (tp)
REVERT: B  297 TRP cc_start: 0.7247 (m100) cc_final: 0.6894 (m100)
REVERT: S  128 MET cc_start: 0.8094 (mmm) cc_final: 0.7627 (mmm)
REVERT: S  217 CYS cc_start: 0.5906 (p) cc_final: 0.5491 (p)
  outliers start: 9
  outliers final: 4
  residues processed: 180
  average time/residue: 0.2098
  time to fit residues: 53.0767
Evaluate side-chains
  146 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 141
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain E residue  159 ILE
Chi-restraints excluded: chain E residue  166 MET
Chi-restraints excluded: chain E residue  169 PRO
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.6980
   chunk 82 optimal weight:    0.2980
   chunk 45 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 85 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9980
   chunk 51 optimal weight:    0.2980
   chunk 63 optimal weight:    0.6980
   chunk 98 optimal weight:    4.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
E  76 ASN
E  92 GLN
E 196 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8904  Z= 0.173
  Angle     :  0.574   6.679  12090  Z= 0.301
  Chirality :  0.042   0.164   1380
  Planarity :  0.004   0.074   1531
  Dihedral  :  4.866  65.765   1216
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 10.22 %
    Favored  : 88.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.28 (0.25), residues: 1104
  helix:  2.04 (0.25), residues: 385
  sheet: -0.50 (0.30), residues: 281
  loop : -0.99 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP E 188 
 HIS   0.006   0.001   HIS E 289 
 PHE   0.022   0.001   PHE E 177 
 TYR   0.016   0.001   TYR S 101 
 ARG   0.004   0.000   ARG B 251 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 173
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6615 (tm-30)
REVERT: A  227 ASP cc_start: 0.7538 (t0) cc_final: 0.7268 (t0)
REVERT: A  244 MET cc_start: 0.9003 (tpp) cc_final: 0.8538 (tpt)
REVERT: B  253 PHE cc_start: 0.7960 (m-80) cc_final: 0.7638 (m-80)
REVERT: B  258 ASP cc_start: 0.6591 (t0) cc_final: 0.6357 (t0)
REVERT: E  195 ARG cc_start: 0.7322 (tmt170) cc_final: 0.6946 (ttp80)
REVERT: S  180 MET cc_start: 0.7113 (ptt) cc_final: 0.6338 (ptt)
REVERT: S  221 LEU cc_start: 0.8528 (tp) cc_final: 0.8229 (tp)
  outliers start: 10
  outliers final: 8
  residues processed: 176
  average time/residue: 0.2108
  time to fit residues: 51.0866
Evaluate side-chains
  155 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 147
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain E residue   36 THR
Chi-restraints excluded: chain E residue  159 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 82 optimal weight:   20.0000
   chunk 67 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 107 optimal weight:    7.9990
   chunk 88 optimal weight:    6.9990
   chunk 98 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
A 307 GLN
A 347 ASN
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   8904  Z= 0.355
  Angle     :  0.635   6.576  12090  Z= 0.336
  Chirality :  0.045   0.179   1380
  Planarity :  0.004   0.067   1531
  Dihedral  :  4.821  72.536   1207
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.59 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.11 (0.25), residues: 1104
  helix:  1.90 (0.25), residues: 387
  sheet: -0.61 (0.30), residues: 282
  loop : -1.09 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP E 188 
 HIS   0.006   0.001   HIS E 263 
 PHE   0.022   0.002   PHE E 177 
 TYR   0.021   0.002   TYR E 200 
 ARG   0.005   0.000   ARG E 133 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6541 (tm-30)
REVERT: A  244 MET cc_start: 0.9043 (tpp) cc_final: 0.8580 (tpt)
REVERT: B  258 ASP cc_start: 0.6644 (t0) cc_final: 0.6425 (t0)
REVERT: B  301 LYS cc_start: 0.5874 (mmtt) cc_final: 0.5643 (mmtt)
REVERT: C   10 LEU cc_start: 0.8593 (mt) cc_final: 0.8137 (tp)
REVERT: E  158 CYS cc_start: 0.7153 (t) cc_final: 0.6944 (t)
REVERT: E  195 ARG cc_start: 0.7240 (tmt170) cc_final: 0.6902 (ttp80)
REVERT: E  197 LYS cc_start: 0.7702 (tppt) cc_final: 0.6898 (tptm)
REVERT: E  250 LEU cc_start: 0.8259 (tp) cc_final: 0.7981 (tp)
REVERT: G   38 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.6027 (pmm)
REVERT: S  101 TYR cc_start: 0.7903 (m-10) cc_final: 0.7617 (m-10)
REVERT: S  128 MET cc_start: 0.8213 (mmm) cc_final: 0.7687 (mmm)
REVERT: S  180 MET cc_start: 0.7577 (ptt) cc_final: 0.7090 (ptt)
REVERT: S  232 LYS cc_start: 0.8606 (tptp) cc_final: 0.8292 (tptt)
  outliers start: 19
  outliers final: 12
  residues processed: 166
  average time/residue: 0.2471
  time to fit residues: 55.7510
Evaluate side-chains
  149 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain E residue   36 THR
Chi-restraints excluded: chain E residue   72 LEU
Chi-restraints excluded: chain E residue  278 THR
Chi-restraints excluded: chain G residue   38 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:   20.0000
   chunk 74 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0370
   chunk 66 optimal weight:    0.9980
   chunk 99 optimal weight:   50.0000
   chunk 105 optimal weight:   10.0000
   chunk 94 optimal weight:    0.3980
   chunk 28 optimal weight:    0.5980
   chunk 87 optimal weight:    0.5980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 347 ASN
S 159 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8904  Z= 0.156
  Angle     :  0.540   6.443  12090  Z= 0.283
  Chirality :  0.041   0.167   1380
  Planarity :  0.004   0.060   1531
  Dihedral  :  4.396  66.606   1205
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.72 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: 1104
  helix:  2.12 (0.25), residues: 391
  sheet: -0.56 (0.31), residues: 267
  loop : -0.94 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP E 188 
 HIS   0.004   0.001   HIS E 289 
 PHE   0.020   0.001   PHE E 177 
 TYR   0.020   0.001   TYR E 200 
 ARG   0.005   0.000   ARG A  10 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 155
  time to evaluate  : 0.999 
Fit side-chains
REVERT: A  244 MET cc_start: 0.8997 (tpp) cc_final: 0.8523 (tpt)
REVERT: E   92 GLN cc_start: 0.8076 (mm110) cc_final: 0.7850 (mp10)
REVERT: E  158 CYS cc_start: 0.6863 (t) cc_final: 0.6595 (t)
REVERT: E  186 PHE cc_start: 0.7625 (m-80) cc_final: 0.7420 (m-80)
REVERT: E  197 LYS cc_start: 0.7648 (tppt) cc_final: 0.7036 (tptm)
REVERT: E  250 LEU cc_start: 0.8191 (tp) cc_final: 0.7966 (tp)
REVERT: G   38 MET cc_start: 0.6324 (OUTLIER) cc_final: 0.5918 (pmm)
REVERT: S   34 MET cc_start: 0.8245 (mmm) cc_final: 0.7996 (mmm)
REVERT: S  180 MET cc_start: 0.7721 (ptt) cc_final: 0.7354 (ptt)
REVERT: S  232 LYS cc_start: 0.8653 (tptp) cc_final: 0.8419 (tptt)
  outliers start: 21
  outliers final: 13
  residues processed: 166
  average time/residue: 0.2120
  time to fit residues: 48.8761
Evaluate side-chains
  164 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 150
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain E residue   36 THR
Chi-restraints excluded: chain E residue   72 LEU
Chi-restraints excluded: chain E residue  163 SER
Chi-restraints excluded: chain E residue  170 VAL
Chi-restraints excluded: chain G residue   38 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0570
   chunk 89 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 53 optimal weight:    6.9990
   chunk 94 optimal weight:    9.9990
   chunk 26 optimal weight:    0.3980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
S 159 ASN
S 174 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8904  Z= 0.161
  Angle     :  0.540   6.749  12090  Z= 0.283
  Chirality :  0.041   0.160   1380
  Planarity :  0.004   0.055   1531
  Dihedral  :  4.371  68.924   1205
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 18.00 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.48 (0.26), residues: 1104
  helix:  2.17 (0.25), residues: 392
  sheet: -0.51 (0.31), residues: 268
  loop : -0.79 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP E 188 
 HIS   0.003   0.001   HIS E 289 
 PHE   0.021   0.001   PHE E 177 
 TYR   0.019   0.001   TYR E 200 
 ARG   0.008   0.000   ARG A  10 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 165
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 MET cc_start: 0.9001 (tpp) cc_final: 0.8538 (tpt)
REVERT: A  313 ARG cc_start: 0.8248 (ttp-110) cc_final: 0.7779 (ptt-90)
REVERT: B  217 MET cc_start: 0.7783 (ptp) cc_final: 0.7139 (ptm)
REVERT: B  219 ARG cc_start: 0.8078 (mmp80) cc_final: 0.7682 (mmp80)
REVERT: E   92 GLN cc_start: 0.8238 (mm110) cc_final: 0.8021 (mp10)
REVERT: E  158 CYS cc_start: 0.6935 (t) cc_final: 0.6707 (t)
REVERT: E  197 LYS cc_start: 0.7680 (tppt) cc_final: 0.7418 (tptp)
REVERT: E  250 LEU cc_start: 0.8283 (tp) cc_final: 0.8059 (tp)
REVERT: G   38 MET cc_start: 0.6249 (OUTLIER) cc_final: 0.5855 (pmm)
REVERT: S   36 TRP cc_start: 0.7841 (m100) cc_final: 0.7515 (m100)
REVERT: S  180 MET cc_start: 0.7767 (ptt) cc_final: 0.7403 (ptt)
  outliers start: 19
  outliers final: 11
  residues processed: 172
  average time/residue: 0.2154
  time to fit residues: 50.9265
Evaluate side-chains
  162 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain E residue   36 THR
Chi-restraints excluded: chain E residue  170 VAL
Chi-restraints excluded: chain E residue  187 CYS
Chi-restraints excluded: chain G residue   38 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 105 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 34 optimal weight:    8.9990
   chunk 55 optimal weight:    7.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 347 ASN
E 190 GLN
S 159 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8904  Z= 0.219
  Angle     :  0.569   8.266  12090  Z= 0.296
  Chirality :  0.042   0.164   1380
  Planarity :  0.004   0.053   1531
  Dihedral  :  4.504  70.977   1205
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 20.13 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.45 (0.26), residues: 1104
  helix:  2.21 (0.25), residues: 386
  sheet: -0.55 (0.30), residues: 279
  loop : -0.82 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E 188 
 HIS   0.004   0.001   HIS E 263 
 PHE   0.021   0.001   PHE E 177 
 TYR   0.017   0.001   TYR E 200 
 ARG   0.008   0.000   ARG A  10 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 MET cc_start: 0.9021 (tpp) cc_final: 0.8558 (tpt)
REVERT: A  309 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7593 (mt-10)
REVERT: A  313 ARG cc_start: 0.8278 (ttp-110) cc_final: 0.7756 (ptt-90)
REVERT: B  217 MET cc_start: 0.7780 (ptp) cc_final: 0.7131 (ptm)
REVERT: B  219 ARG cc_start: 0.8081 (mmp80) cc_final: 0.7721 (mmp80)
REVERT: E  158 CYS cc_start: 0.6945 (t) cc_final: 0.6703 (t)
REVERT: E  187 CYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6762 (t)
REVERT: E  197 LYS cc_start: 0.7657 (tppt) cc_final: 0.7128 (tptp)
REVERT: E  250 LEU cc_start: 0.8277 (tp) cc_final: 0.8026 (tp)
REVERT: G   38 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.5835 (pmm)
REVERT: S   36 TRP cc_start: 0.7889 (m100) cc_final: 0.7547 (m100)
REVERT: S  128 MET cc_start: 0.8083 (mtp) cc_final: 0.7448 (mmm)
REVERT: S  180 MET cc_start: 0.7741 (ptt) cc_final: 0.7507 (ptt)
REVERT: S  232 LYS cc_start: 0.8639 (tptt) cc_final: 0.8435 (tptt)
  outliers start: 18
  outliers final: 13
  residues processed: 160
  average time/residue: 0.2346
  time to fit residues: 52.3897
Evaluate side-chains
  170 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain E residue   36 THR
Chi-restraints excluded: chain E residue  170 VAL
Chi-restraints excluded: chain E residue  187 CYS
Chi-restraints excluded: chain E residue  278 THR
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain S residue  143 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9980
   chunk 65 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 347 ASN
E  92 GLN
E 174 GLN
S 159 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7010
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8904  Z= 0.189
  Angle     :  0.558   7.976  12090  Z= 0.289
  Chirality :  0.041   0.156   1380
  Planarity :  0.004   0.052   1531
  Dihedral  :  4.433  69.335   1205
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 20.13 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.50 (0.26), residues: 1104
  helix:  2.27 (0.25), residues: 386
  sheet: -0.54 (0.31), residues: 269
  loop : -0.80 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP S 164 
 HIS   0.003   0.001   HIS E 228 
 PHE   0.023   0.001   PHE E 177 
 TYR   0.015   0.001   TYR S 178 
 ARG   0.009   0.000   ARG A  10 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 GLU cc_start: 0.8092 (mp0) cc_final: 0.7856 (mp0)
REVERT: A  244 MET cc_start: 0.9016 (tpp) cc_final: 0.8546 (tpt)
REVERT: A  309 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7623 (mt-10)
REVERT: A  313 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.7687 (ptt-90)
REVERT: B  217 MET cc_start: 0.7692 (ptp) cc_final: 0.7072 (ptm)
REVERT: B  219 ARG cc_start: 0.8058 (mmp80) cc_final: 0.7658 (mmp80)
REVERT: B  253 PHE cc_start: 0.7883 (m-80) cc_final: 0.7648 (m-80)
REVERT: E  158 CYS cc_start: 0.6935 (t) cc_final: 0.6686 (t)
REVERT: E  187 CYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6803 (t)
REVERT: E  197 LYS cc_start: 0.7545 (tppt) cc_final: 0.6879 (tptp)
REVERT: E  250 LEU cc_start: 0.8260 (tp) cc_final: 0.8029 (tp)
REVERT: G   38 MET cc_start: 0.6244 (OUTLIER) cc_final: 0.5832 (pmm)
REVERT: S   36 TRP cc_start: 0.7863 (m100) cc_final: 0.7544 (m100)
REVERT: S  128 MET cc_start: 0.7995 (mtp) cc_final: 0.7786 (mmm)
REVERT: S  180 MET cc_start: 0.7743 (ptt) cc_final: 0.7524 (ptt)
  outliers start: 24
  outliers final: 18
  residues processed: 171
  average time/residue: 0.2145
  time to fit residues: 50.0542
Evaluate side-chains
  168 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain E residue   36 THR
Chi-restraints excluded: chain E residue  131 VAL
Chi-restraints excluded: chain E residue  166 MET
Chi-restraints excluded: chain E residue  170 VAL
Chi-restraints excluded: chain E residue  187 CYS
Chi-restraints excluded: chain E residue  275 PHE
Chi-restraints excluded: chain E residue  278 THR
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  143 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   chunk 82 optimal weight:    9.9990
   chunk 95 optimal weight:   10.0000
   chunk 100 optimal weight:    5.9990
   chunk 91 optimal weight:    0.8980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 347 ASN
B  88 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8904  Z= 0.257
  Angle     :  0.597  10.092  12090  Z= 0.310
  Chirality :  0.042   0.160   1380
  Planarity :  0.004   0.051   1531
  Dihedral  :  4.610  71.876   1205
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 20.13 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.26), residues: 1104
  helix:  2.16 (0.25), residues: 385
  sheet: -0.63 (0.31), residues: 275
  loop : -0.78 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E 188 
 HIS   0.004   0.001   HIS E 263 
 PHE   0.023   0.002   PHE E 177 
 TYR   0.016   0.002   TYR E 200 
 ARG   0.010   0.000   ARG A  10 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 MET cc_start: 0.9040 (tpp) cc_final: 0.8571 (tpt)
REVERT: A  309 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7648 (mt-10)
REVERT: A  313 ARG cc_start: 0.8320 (ttp-110) cc_final: 0.7624 (ptt-90)
REVERT: B  217 MET cc_start: 0.7676 (ptp) cc_final: 0.6979 (ptm)
REVERT: B  219 ARG cc_start: 0.8077 (mmp80) cc_final: 0.7633 (mmp80)
REVERT: E  158 CYS cc_start: 0.6989 (t) cc_final: 0.6694 (t)
REVERT: E  187 CYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6774 (t)
REVERT: E  197 LYS cc_start: 0.7561 (tppt) cc_final: 0.7155 (tptp)
REVERT: E  250 LEU cc_start: 0.8231 (tp) cc_final: 0.7976 (tp)
REVERT: G   38 MET cc_start: 0.6322 (OUTLIER) cc_final: 0.5914 (pmm)
REVERT: S   36 TRP cc_start: 0.7928 (m100) cc_final: 0.7638 (m100)
REVERT: S  128 MET cc_start: 0.8229 (mtp) cc_final: 0.7759 (tpp)
REVERT: S  180 MET cc_start: 0.7775 (ptt) cc_final: 0.7529 (ptt)
  outliers start: 25
  outliers final: 17
  residues processed: 166
  average time/residue: 0.2194
  time to fit residues: 50.2438
Evaluate side-chains
  172 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 153
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain E residue   36 THR
Chi-restraints excluded: chain E residue  131 VAL
Chi-restraints excluded: chain E residue  170 VAL
Chi-restraints excluded: chain E residue  187 CYS
Chi-restraints excluded: chain E residue  275 PHE
Chi-restraints excluded: chain E residue  278 THR
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  143 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   chunk 58 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 103 optimal weight:    7.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 347 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7015
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8904  Z= 0.188
  Angle     :  0.582   9.035  12090  Z= 0.301
  Chirality :  0.042   0.194   1380
  Planarity :  0.004   0.051   1531
  Dihedral  :  4.467  68.520   1205
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.66 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: 1104
  helix:  2.17 (0.26), residues: 386
  sheet: -0.58 (0.30), residues: 275
  loop : -0.77 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 188 
 HIS   0.003   0.001   HIS E 112 
 PHE   0.025   0.001   PHE E 177 
 TYR   0.015   0.001   TYR S 178 
 ARG   0.009   0.000   ARG A  10 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7652 (mt-10)
REVERT: A  313 ARG cc_start: 0.8305 (ttp-110) cc_final: 0.7626 (ptt-90)
REVERT: B  217 MET cc_start: 0.7680 (ptp) cc_final: 0.7018 (ptm)
REVERT: B  219 ARG cc_start: 0.8039 (mmp80) cc_final: 0.7692 (mmp80)
REVERT: E  101 TRP cc_start: 0.7272 (t-100) cc_final: 0.6949 (t-100)
REVERT: E  158 CYS cc_start: 0.6941 (t) cc_final: 0.6685 (t)
REVERT: E  187 CYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6778 (t)
REVERT: E  189 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7893 (mm-30)
REVERT: E  197 LYS cc_start: 0.7489 (tppt) cc_final: 0.7060 (tptp)
REVERT: E  250 LEU cc_start: 0.8257 (tp) cc_final: 0.8020 (tp)
REVERT: G   38 MET cc_start: 0.6297 (OUTLIER) cc_final: 0.5892 (pmm)
REVERT: S   36 TRP cc_start: 0.7892 (m100) cc_final: 0.7615 (m100)
REVERT: S   38 ARG cc_start: 0.6564 (ptp-170) cc_final: 0.6226 (ptp-110)
REVERT: S  128 MET cc_start: 0.8132 (mtp) cc_final: 0.7880 (mmm)
REVERT: S  180 MET cc_start: 0.7728 (ptt) cc_final: 0.7514 (ptt)
REVERT: S  200 PHE cc_start: 0.6486 (m-80) cc_final: 0.6109 (m-10)
REVERT: S  232 LYS cc_start: 0.8663 (tptt) cc_final: 0.8457 (tptt)
  outliers start: 27
  outliers final: 21
  residues processed: 168
  average time/residue: 0.2121
  time to fit residues: 49.2944
Evaluate side-chains
  169 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 1.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain E residue   36 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  131 VAL
Chi-restraints excluded: chain E residue  170 VAL
Chi-restraints excluded: chain E residue  187 CYS
Chi-restraints excluded: chain E residue  275 PHE
Chi-restraints excluded: chain E residue  278 THR
Chi-restraints excluded: chain E residue  294 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  175 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0060
   chunk 108 optimal weight:    3.9990
   chunk 99 optimal weight:    8.9990
   chunk 86 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0050
   chunk 66 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 68 optimal weight:    0.6980
   chunk 92 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.5414

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 347 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7054
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8904  Z= 0.240
  Angle     :  0.606   8.822  12090  Z= 0.315
  Chirality :  0.042   0.160   1380
  Planarity :  0.004   0.050   1531
  Dihedral  :  4.608  70.934   1205
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 21.30 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: 1104
  helix:  2.07 (0.26), residues: 386
  sheet: -0.63 (0.31), residues: 275
  loop : -0.79 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E 188 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.026   0.002   PHE E 177 
 TYR   0.016   0.002   TYR B 105 
 ARG   0.011   0.000   ARG A  10 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7614 (mt-10)
REVERT: A  313 ARG cc_start: 0.8267 (ttp-110) cc_final: 0.7586 (ptt-90)
REVERT: B   59 TYR cc_start: 0.8700 (m-80) cc_final: 0.8297 (m-80)
REVERT: B  217 MET cc_start: 0.7634 (ptp) cc_final: 0.7018 (ptm)
REVERT: B  219 ARG cc_start: 0.8043 (mmp80) cc_final: 0.7735 (mmp80)
REVERT: E   92 GLN cc_start: 0.7641 (mp10) cc_final: 0.7384 (mp10)
REVERT: E  101 TRP cc_start: 0.7366 (t-100) cc_final: 0.7038 (t-100)
REVERT: E  158 CYS cc_start: 0.7096 (t) cc_final: 0.6773 (t)
REVERT: E  197 LYS cc_start: 0.7545 (tppt) cc_final: 0.7034 (tptp)
REVERT: E  250 LEU cc_start: 0.8218 (tp) cc_final: 0.7968 (tp)
REVERT: G   38 MET cc_start: 0.6328 (OUTLIER) cc_final: 0.5906 (pmm)
REVERT: S   36 TRP cc_start: 0.7919 (m100) cc_final: 0.7643 (m100)
REVERT: S   38 ARG cc_start: 0.6578 (ptp-170) cc_final: 0.6354 (ptp-110)
REVERT: S  128 MET cc_start: 0.8155 (mtp) cc_final: 0.7617 (tpp)
REVERT: S  180 MET cc_start: 0.7738 (ptt) cc_final: 0.7472 (ptt)
REVERT: S  232 LYS cc_start: 0.8635 (tptt) cc_final: 0.8380 (tptt)
  outliers start: 24
  outliers final: 21
  residues processed: 160
  average time/residue: 0.2165
  time to fit residues: 47.7974
Evaluate side-chains
  169 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain E residue   36 THR
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue  131 VAL
Chi-restraints excluded: chain E residue  170 VAL
Chi-restraints excluded: chain E residue  187 CYS
Chi-restraints excluded: chain E residue  275 PHE
Chi-restraints excluded: chain E residue  278 THR
Chi-restraints excluded: chain E residue  294 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  175 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0870
   chunk 62 optimal weight:    0.9980
   overall best weight:    1.4164

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 347 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.197665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.156242 restraints weight = 11373.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3973 rms_B_bonded: 3.17
r_work: 0.3729 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8904  Z= 0.232
  Angle     :  0.606   8.564  12090  Z= 0.316
  Chirality :  0.042   0.154   1380
  Planarity :  0.004   0.050   1531
  Dihedral  :  4.606  69.573   1205
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 21.19 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: 1104
  helix:  2.08 (0.25), residues: 386
  sheet: -0.63 (0.31), residues: 275
  loop : -0.82 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E 188 
 HIS   0.004   0.001   HIS E 112 
 PHE   0.026   0.001   PHE E 177 
 TYR   0.016   0.002   TYR B 289 
 ARG   0.011   0.000   ARG A  10 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2055.54 seconds
wall clock time: 38 minutes 38.83 seconds (2318.83 seconds total)