Starting phenix.real_space_refine
on Mon May 12 00:32:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8eit_28164/05_2025/8eit_28164.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8eit_28164/05_2025/8eit_28164.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8eit_28164/05_2025/8eit_28164.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8eit_28164/05_2025/8eit_28164.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8eit_28164/05_2025/8eit_28164.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8eit_28164/05_2025/8eit_28164.cif"
  }
  resolution = 2.8
  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=   0.000 sd=   0.003
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      49      5.16       5
     C    5453      2.51       5
     N    1480      2.21       5
     O    1596      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8578
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1821
          Classifications: {'peptide': 226}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 5, 'TRANS': 220}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 2565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2565
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "C"
      Number of atoms: 422
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 422
          Classifications: {'peptide': 59}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 4, 'TRANS': 54}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "E"
      Number of atoms: 1800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1800
          Classifications: {'peptide': 234}
          Link IDs: {'PTRANS': 10, 'TRANS': 223}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 1961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 1961
          Classifications: {'peptide': 268}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 20, 'TRANS': 247}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 24
    Chain: "R"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Unusual residues: {'HXA': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'HXA:plan-3': 1, 'HXA:plan-5': 1, 'HXA:plan-4': 1, 'HXA:plan-7': 1, 'HXA:plan-6': 1}
          Unresolved non-hydrogen planarities: 18
  Time building chain proxies: 4.91, per 1000 atoms: 0.57
  Number of scatterers: 8578
  At special positions: 0
  Unit cell: (100.44, 119.88, 125.28, 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      49     16.00
     O    1596      8.00
     N    1480      7.00
     C    5453      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.04

  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: 2.14
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2072

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 14 sheets defined
      38.4% alpha, 23.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 4.111A  pdb=" N   THR A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 89
      removed outlier: 4.403A  pdb=" N   TRP A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A  89 " --> pdb=" O   ARG A  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 84 through 89'
    Processing helix  chain 'A' and resid 90 through 93
      removed outlier: 3.829A  pdb=" N   ASN A  93 " --> pdb=" O   GLN A  90 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 90 through 93'
    Processing helix  chain 'A' and resid 109 through 122
    Processing helix  chain 'A' and resid 137 through 148
    Processing helix  chain 'A' and resid 151 through 155
    Processing helix  chain 'A' and resid 156 through 162
    Processing helix  chain 'A' and resid 175 through 196
      removed outlier: 3.687A  pdb=" N   PHE A 189 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   SER A 196 " --> pdb=" O   ILE A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 235
    Processing helix  chain 'B' and resid 6 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.534A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 26
    Processing helix  chain 'C' and resid 29 through 42
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 4.209A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 62 through 65
      removed outlier: 3.564A  pdb=" N   LYS E  65 " --> pdb=" O   ASP E  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 62 through 65'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.569A  pdb=" N   ASP E  90 " --> pdb=" O   ARG E  87 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 87 through 91'
    Processing helix  chain 'E' and resid 220 through 224
      removed outlier: 4.030A  pdb=" N   VAL E 224 " --> pdb=" O   ALA E 221 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 4 through 37
      Proline residue:  R  21  - end of helix
      removed outlier: 4.000A  pdb=" N   LEU R  36 " --> pdb=" O   ALA R  32 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ARG R  37 " --> pdb=" O   HIS R  33 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 39 through 68
      Proline residue:  R  60  - end of helix
      removed outlier: 3.585A  pdb=" N   ALA R  68 " --> pdb=" O   VAL R  64 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 75 through 77
      No H-bonds generated for 'chain 'R' and resid 75 through 77'
    Processing helix  chain 'R' and resid 78 through 87
      removed outlier: 3.534A  pdb=" N   PHE R  82 " --> pdb=" O   LEU R  78 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   ALA R  85 " --> pdb=" O   VAL R  81 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 88 through 107
      removed outlier: 5.270A  pdb=" N   GLY R  94 " --> pdb=" O   LEU R  90 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   GLY R  95 " --> pdb=" O   TYR R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 110 through 117
    Processing helix  chain 'R' and resid 119 through 143
      removed outlier: 3.511A  pdb=" N   SER R 123 " --> pdb=" O   ARG R 119 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 175 through 191
      Proline residue:  R 181  - end of helix
    Processing helix  chain 'R' and resid 191 through 212
    Processing helix  chain 'R' and resid 215 through 226
    Processing helix  chain 'R' and resid 226 through 236
      removed outlier: 4.667A  pdb=" N   LEU R 230 " --> pdb=" O   ALA R 226 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 236 through 250
      removed outlier: 4.192A  pdb=" N   TYR R 240 " --> pdb=" O   CYS R 236 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 255 through 272
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 68
      removed outlier: 4.686A  pdb=" N   VAL A  78 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ALA A  97 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.266A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 6.908A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.024A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.565A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.509A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.382A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.668A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.737A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 4.000A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 149
      removed outlier: 4.182A  pdb=" N   GLU E 246 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   VAL E 149 " --> pdb=" O   GLU E 246 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 160 through 161
      removed outlier: 3.586A  pdb=" N   VAL R 169 " --> pdb=" O   ASN R 161 " (cutoff:3.500A)

    457 hydrogen bonds defined for protein.
    1284 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: 2.42

  Time building geometry restraints manager: 2.46 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2792
        1.34 -     1.46: 2064
        1.46 -     1.58: 3843
        1.58 -     1.70: 0
        1.70 -     1.82: 66
  Bond restraints: 8765
  Sorted by residual:
  bond pdb=" C4  HXA R 401 "
       pdb=" C5  HXA R 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.531 -0.199 2.00e-02 2.50e+03 9.93e+01
  bond pdb=" C3  HXA R 401 "
       pdb=" C4  HXA R 401 "
    ideal  model  delta    sigma   weight residual
    1.496  1.530 -0.034 2.00e-02 2.50e+03 2.93e+00
  bond pdb=" C5  HXA R 401 "
       pdb=" C6  HXA R 401 "
    ideal  model  delta    sigma   weight residual
    1.503  1.529 -0.026 2.00e-02 2.50e+03 1.70e+00
  bond pdb=" C6  HXA R 401 "
       pdb=" C7  HXA R 401 "
    ideal  model  delta    sigma   weight residual
    1.502  1.527 -0.025 2.00e-02 2.50e+03 1.57e+00
  bond pdb=" CG1 ILE R 130 "
       pdb=" CD1 ILE R 130 "
    ideal  model  delta    sigma   weight residual
    1.513  1.467  0.046 3.90e-02 6.57e+02 1.40e+00
  ... (remaining 8760 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 11762
        2.57 -     5.15: 117
        5.15 -     7.72: 22
        7.72 -    10.30: 3
       10.30 -    12.87: 2
  Bond angle restraints: 11906
  Sorted by residual:
  angle pdb=" C3  HXA R 401 "
        pdb=" C4  HXA R 401 "
        pdb=" C5  HXA R 401 "
      ideal   model   delta    sigma   weight residual
     128.39  115.52   12.87 3.00e+00 1.11e-01 1.84e+01
  angle pdb=" C4  HXA R 401 "
        pdb=" C5  HXA R 401 "
        pdb=" C6  HXA R 401 "
      ideal   model   delta    sigma   weight residual
     127.44  115.45   11.99 3.00e+00 1.11e-01 1.60e+01
  angle pdb=" N   ASP C  48 "
        pdb=" CA  ASP C  48 "
        pdb=" C   ASP C  48 "
      ideal   model   delta    sigma   weight residual
     109.64  114.51   -4.87 1.27e+00 6.20e-01 1.47e+01
  angle pdb=" N   ARG C  13 "
        pdb=" CA  ARG C  13 "
        pdb=" CB  ARG C  13 "
      ideal   model   delta    sigma   weight residual
     110.12  115.34   -5.22 1.47e+00 4.63e-01 1.26e+01
  angle pdb=" C   ALA C  10 "
        pdb=" N   GLN C  11 "
        pdb=" CA  GLN C  11 "
      ideal   model   delta    sigma   weight residual
     121.18  114.98    6.20 1.98e+00 2.55e-01 9.82e+00
  ... (remaining 11901 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.83: 4659
       16.83 -    33.67: 400
       33.67 -    50.50: 77
       50.50 -    67.33: 9
       67.33 -    84.17: 10
  Dihedral angle restraints: 5155
    sinusoidal: 1932
      harmonic: 3223
  Sorted by residual:
  dihedral pdb=" CA  TYR E 101 "
           pdb=" C   TYR E 101 "
           pdb=" N   TYR E 102 "
           pdb=" CA  TYR E 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.08   17.92     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  LEU R  59 "
           pdb=" C   LEU R  59 "
           pdb=" N   PRO R  60 "
           pdb=" CA  PRO R  60 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.60  -17.40     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CA  PHE R  82 "
           pdb=" C   PHE R  82 "
           pdb=" N   ALA R  83 "
           pdb=" CA  ALA R  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.09  -16.91     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 5152 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1043
       0.050 -    0.100: 235
       0.100 -    0.150: 62
       0.150 -    0.200: 6
       0.200 -    0.250: 3
  Chirality restraints: 1349
  Sorted by residual:
  chirality pdb=" CB  THR A 169 "
            pdb=" CA  THR A 169 "
            pdb=" OG1 THR A 169 "
            pdb=" CG2 THR A 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.30    0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CB  THR E  91 "
            pdb=" CA  THR E  91 "
            pdb=" OG1 THR E  91 "
            pdb=" CG2 THR E  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.24 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CB  ILE C   9 "
            pdb=" CA  ILE C   9 "
            pdb=" CG1 ILE C   9 "
            pdb=" CG2 ILE C   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.19e+00
  ... (remaining 1346 not shown)

  Planarity restraints: 1523
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E  74 "   -0.042 5.00e-02 4.00e+02   6.32e-02 6.38e+00
        pdb=" N   PRO E  75 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO E  75 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO E  75 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  48 "    0.041 5.00e-02 4.00e+02   6.25e-02 6.24e+00
        pdb=" N   PRO C  49 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO C  49 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C  49 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 238 "   -0.038 5.00e-02 4.00e+02   5.80e-02 5.39e+00
        pdb=" N   PRO R 239 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO R 239 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO R 239 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1520 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1358
        2.76 -     3.30: 7951
        3.30 -     3.83: 14467
        3.83 -     4.37: 16781
        4.37 -     4.90: 29308
  Nonbonded interactions: 69865
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OH  TYR R 240 "
            pdb=" O1  HXA R 401 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OG  SER E 161 "
            pdb=" O   LYS E 163 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OG  SER R 268 "
            pdb=" OD1 ASN R 272 "
     model   vdw
     2.319 3.040
  ... (remaining 69860 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:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     21.320
  Find NCS groups from input model:        0.100
  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:             0.010
  Load rotamer database and sin/cos tables:10.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
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   0.199   8766  Z= 0.177
  Angle     :  0.685  12.870  11908  Z= 0.351
  Chirality :  0.047   0.250   1349
  Planarity :  0.005   0.063   1523
  Dihedral  : 13.351  84.169   3080
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.33 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.26), residues: 1101
  helix:  1.64 (0.26), residues: 370
  sheet:  1.01 (0.32), residues: 250
  loop : -0.03 (0.30), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 339 
 HIS   0.009   0.001   HIS R  86 
 PHE   0.021   0.002   PHE R  82 
 TYR   0.024   0.001   TYR E 190 
 ARG   0.015   0.000   ARG C  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12451 (  450)
  hydrogen bonds       : angle       5.82093 ( 1284)
  SS BOND              : bond        0.00513 (    1)
  SS BOND              : angle       1.10121 (    2)
  covalent geometry    : bond        0.00355 ( 8765)
  covalent geometry    : angle       0.68458 (11906)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 187
  time to evaluate  : 0.871 
Fit side-chains
REVERT: R  137 HIS cc_start: 0.7464 (m-70) cc_final: 0.6614 (m-70)
  outliers start: 1
  outliers final: 1
  residues processed: 188
  average time/residue: 1.1866
  time to fit residues: 237.4088
Evaluate side-chains
  143 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0770
   chunk 28 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 85 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 98 optimal weight:    8.9990
   overall best weight:    1.7742

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
A 215 ASN
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN
B  75 GLN
B 155 ASN
R 272 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.134375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.099069 restraints weight = 13408.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.50
r_work: 0.3161 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.1593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8766  Z= 0.169
  Angle     :  0.598  10.017  11908  Z= 0.309
  Chirality :  0.044   0.281   1349
  Planarity :  0.005   0.067   1523
  Dihedral  :  5.347  77.722   1220
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.41 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.26), residues: 1101
  helix:  2.24 (0.27), residues: 384
  sheet:  0.90 (0.32), residues: 262
  loop :  0.07 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 131 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.014   0.002   PHE B 234 
 TYR   0.022   0.002   TYR E 190 
 ARG   0.007   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04103 (  450)
  hydrogen bonds       : angle       4.57404 ( 1284)
  SS BOND              : bond        0.00869 (    1)
  SS BOND              : angle       2.73606 (    2)
  covalent geometry    : bond        0.00386 ( 8765)
  covalent geometry    : angle       0.59739 (11906)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 160
  time to evaluate  : 0.900 
Fit side-chains
REVERT: B  254 ASP cc_start: 0.8761 (t0) cc_final: 0.8534 (t0)
REVERT: C   32 LYS cc_start: 0.8778 (tppt) cc_final: 0.8096 (tppt)
REVERT: E   87 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7150 (mmt90)
REVERT: E  223 ASP cc_start: 0.7344 (m-30) cc_final: 0.6847 (m-30)
REVERT: R    6 GLN cc_start: 0.8206 (mp10) cc_final: 0.7856 (mt0)
REVERT: R   52 ASP cc_start: 0.8049 (t70) cc_final: 0.7808 (t70)
REVERT: R  137 HIS cc_start: 0.7590 (m-70) cc_final: 0.6770 (m-70)
REVERT: R  188 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8883 (mp)
REVERT: R  259 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8660 (mtpp)
  outliers start: 18
  outliers final: 8
  residues processed: 170
  average time/residue: 1.1551
  time to fit residues: 209.0773
Evaluate side-chains
  156 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 146
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain E residue   39 GLN
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue   98 ARG
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   62 LYS
Chi-restraints excluded: chain R residue  188 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 85 optimal weight:    8.9990
   chunk 36 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN
B 155 ASN
R  23 ASN
R 244 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.133602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.098096 restraints weight = 13446.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 2.51
r_work: 0.3148 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8766  Z= 0.153
  Angle     :  0.565   6.962  11908  Z= 0.295
  Chirality :  0.043   0.176   1349
  Planarity :  0.004   0.058   1523
  Dihedral  :  4.742  58.550   1218
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 16.74 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.26), residues: 1101
  helix:  2.33 (0.27), residues: 385
  sheet:  0.88 (0.31), residues: 268
  loop :  0.05 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 131 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.012   0.002   PHE B 199 
 TYR   0.022   0.001   TYR E 190 
 ARG   0.008   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  450)
  hydrogen bonds       : angle       4.39591 ( 1284)
  SS BOND              : bond        0.00563 (    1)
  SS BOND              : angle       1.52331 (    2)
  covalent geometry    : bond        0.00347 ( 8765)
  covalent geometry    : angle       0.56467 (11906)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 151
  time to evaluate  : 0.887 
Fit side-chains
REVERT: C   19 LEU cc_start: 0.6698 (tp) cc_final: 0.6493 (tp)
REVERT: C   32 LYS cc_start: 0.8603 (tppt) cc_final: 0.8207 (tppt)
REVERT: E   87 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7144 (mmt90)
REVERT: R   23 ASN cc_start: 0.8381 (m-40) cc_final: 0.7936 (m110)
REVERT: R   52 ASP cc_start: 0.7987 (t70) cc_final: 0.7776 (t70)
REVERT: R  137 HIS cc_start: 0.7607 (m-70) cc_final: 0.6780 (m-70)
REVERT: R  188 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8881 (mp)
REVERT: R  218 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7832 (mtt90)
REVERT: R  259 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8676 (mtpp)
  outliers start: 24
  outliers final: 11
  residues processed: 163
  average time/residue: 1.1705
  time to fit residues: 203.1621
Evaluate side-chains
  157 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ARG
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain E residue   39 GLN
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue   98 ARG
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   62 LYS
Chi-restraints excluded: chain R residue  188 LEU
Chi-restraints excluded: chain R residue  218 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 61 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 101 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 71 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 62 optimal weight:    0.5980
   chunk 44 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN
B 155 ASN
B 220 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 244 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.134280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.098934 restraints weight = 13338.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.51
r_work: 0.3161 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8766  Z= 0.125
  Angle     :  0.535   7.431  11908  Z= 0.279
  Chirality :  0.042   0.165   1349
  Planarity :  0.004   0.059   1523
  Dihedral  :  4.503  56.901   1218
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 17.41 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.26), residues: 1101
  helix:  2.53 (0.27), residues: 379
  sheet:  0.99 (0.31), residues: 259
  loop :  0.14 (0.31), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 131 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.025   0.001   PHE R 200 
 TYR   0.020   0.001   TYR E 190 
 ARG   0.011   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03530 (  450)
  hydrogen bonds       : angle       4.24045 ( 1284)
  SS BOND              : bond        0.00244 (    1)
  SS BOND              : angle       1.22596 (    2)
  covalent geometry    : bond        0.00280 ( 8765)
  covalent geometry    : angle       0.53472 (11906)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 156
  time to evaluate  : 0.967 
Fit side-chains
REVERT: C   19 LEU cc_start: 0.6693 (tp) cc_final: 0.6472 (tp)
REVERT: C   32 LYS cc_start: 0.8439 (tppt) cc_final: 0.8129 (tppt)
REVERT: E   87 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7167 (mmt90)
REVERT: E  219 LEU cc_start: 0.8293 (mp) cc_final: 0.7571 (tt)
REVERT: E  223 ASP cc_start: 0.7291 (m-30) cc_final: 0.6507 (m-30)
REVERT: R    6 GLN cc_start: 0.8250 (mp10) cc_final: 0.8011 (mt0)
REVERT: R  135 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8092 (mm)
REVERT: R  137 HIS cc_start: 0.7723 (m-70) cc_final: 0.6878 (m-70)
REVERT: R  188 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8877 (mp)
REVERT: R  202 TYR cc_start: 0.9304 (t80) cc_final: 0.9096 (t80)
REVERT: R  218 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7849 (mtt90)
REVERT: R  259 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8684 (mtpp)
  outliers start: 26
  outliers final: 10
  residues processed: 170
  average time/residue: 1.1953
  time to fit residues: 216.1388
Evaluate side-chains
  157 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain E residue   39 GLN
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue   98 ARG
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue   62 LYS
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  188 LEU
Chi-restraints excluded: chain R residue  218 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 44 optimal weight:    6.9990
   chunk 102 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:    0.4980
   chunk 37 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 60 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN
B 155 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  23 ASN
R 244 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.135002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.099809 restraints weight = 13232.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 2.49
r_work: 0.3175 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8766  Z= 0.113
  Angle     :  0.527   7.512  11908  Z= 0.275
  Chirality :  0.042   0.161   1349
  Planarity :  0.004   0.058   1523
  Dihedral  :  4.341  54.061   1218
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 18.40 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.26), residues: 1101
  helix:  2.61 (0.27), residues: 378
  sheet:  1.05 (0.32), residues: 258
  loop :  0.14 (0.30), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 131 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.015   0.001   PHE R 200 
 TYR   0.018   0.001   TYR E 190 
 ARG   0.011   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03388 (  450)
  hydrogen bonds       : angle       4.15768 ( 1284)
  SS BOND              : bond        0.00538 (    1)
  SS BOND              : angle       0.78931 (    2)
  covalent geometry    : bond        0.00252 ( 8765)
  covalent geometry    : angle       0.52657 (11906)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 152
  time to evaluate  : 0.906 
Fit side-chains
REVERT: A  222 ASP cc_start: 0.8696 (m-30) cc_final: 0.8464 (m-30)
REVERT: C   19 LEU cc_start: 0.6701 (tp) cc_final: 0.6476 (tp)
REVERT: C   32 LYS cc_start: 0.8418 (tppt) cc_final: 0.8025 (tppt)
REVERT: C   36 ASP cc_start: 0.8545 (m-30) cc_final: 0.8323 (m-30)
REVERT: E   46 GLU cc_start: 0.8489 (tt0) cc_final: 0.8208 (pt0)
REVERT: E  219 LEU cc_start: 0.8291 (mp) cc_final: 0.7594 (tt)
REVERT: R   53 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8613 (tp)
REVERT: R  135 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8041 (mm)
REVERT: R  137 HIS cc_start: 0.7748 (m-70) cc_final: 0.6894 (m-70)
REVERT: R  188 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8899 (mp)
REVERT: R  218 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7864 (mtt90)
REVERT: R  259 LYS cc_start: 0.8979 (mtpt) cc_final: 0.8679 (mtpp)
  outliers start: 26
  outliers final: 13
  residues processed: 168
  average time/residue: 1.1386
  time to fit residues: 204.0989
Evaluate side-chains
  159 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ARG
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue   98 ARG
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   62 LYS
Chi-restraints excluded: chain R residue  133 LEU
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  188 LEU
Chi-restraints excluded: chain R residue  218 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 61 optimal weight:    0.0570
   chunk 94 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 73 optimal weight:   50.0000
   chunk 65 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    1.3500

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN
B 155 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  23 ASN
R 244 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.133516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.098238 restraints weight = 13221.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 2.48
r_work: 0.3151 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8766  Z= 0.140
  Angle     :  0.552   7.648  11908  Z= 0.288
  Chirality :  0.043   0.215   1349
  Planarity :  0.004   0.058   1523
  Dihedral  :  4.446  52.404   1218
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 19.18 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.26), residues: 1101
  helix:  2.54 (0.27), residues: 379
  sheet:  0.96 (0.32), residues: 261
  loop :  0.21 (0.31), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 131 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.013   0.001   PHE B 253 
 TYR   0.019   0.001   TYR E 190 
 ARG   0.016   0.001   ARG A 161 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03563 (  450)
  hydrogen bonds       : angle       4.19073 ( 1284)
  SS BOND              : bond        0.00444 (    1)
  SS BOND              : angle       0.86669 (    2)
  covalent geometry    : bond        0.00320 ( 8765)
  covalent geometry    : angle       0.55202 (11906)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 147
  time to evaluate  : 0.884 
Fit side-chains
REVERT: C   19 LEU cc_start: 0.6729 (tp) cc_final: 0.6502 (tp)
REVERT: C   32 LYS cc_start: 0.8451 (tppt) cc_final: 0.8098 (tppt)
REVERT: E   46 GLU cc_start: 0.8497 (tt0) cc_final: 0.8236 (pt0)
REVERT: E   87 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7176 (mmt90)
REVERT: R    6 GLN cc_start: 0.8441 (mp10) cc_final: 0.8192 (mt0)
REVERT: R   53 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8594 (tp)
REVERT: R  135 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8062 (mm)
REVERT: R  137 HIS cc_start: 0.7719 (m-70) cc_final: 0.6862 (m-70)
REVERT: R  188 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8876 (mp)
REVERT: R  259 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8658 (mtpp)
  outliers start: 31
  outliers final: 15
  residues processed: 167
  average time/residue: 1.1980
  time to fit residues: 213.1271
Evaluate side-chains
  160 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ARG
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain E residue   39 GLN
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue   98 ARG
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   62 LYS
Chi-restraints excluded: chain R residue   79 CYS
Chi-restraints excluded: chain R residue  133 LEU
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  188 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 76 optimal weight:    0.7980
   chunk 98 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   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  74 HIS
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN
B 155 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  23 ASN
R 244 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.134220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.099011 restraints weight = 13357.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.50
r_work: 0.3164 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8766  Z= 0.122
  Angle     :  0.560   7.851  11908  Z= 0.290
  Chirality :  0.042   0.179   1349
  Planarity :  0.004   0.058   1523
  Dihedral  :  4.352  50.104   1218
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 19.29 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.26), residues: 1101
  helix:  2.61 (0.27), residues: 378
  sheet:  1.01 (0.31), residues: 258
  loop :  0.20 (0.31), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 131 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.018   0.001   TYR E 190 
 ARG   0.011   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03395 (  450)
  hydrogen bonds       : angle       4.14914 ( 1284)
  SS BOND              : bond        0.00430 (    1)
  SS BOND              : angle       0.55599 (    2)
  covalent geometry    : bond        0.00276 ( 8765)
  covalent geometry    : angle       0.55970 (11906)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 1.028 
Fit side-chains
REVERT: B  260 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8258 (tm-30)
REVERT: C   32 LYS cc_start: 0.8532 (tppt) cc_final: 0.8313 (tppt)
REVERT: E   46 GLU cc_start: 0.8493 (tt0) cc_final: 0.8220 (pt0)
REVERT: E   87 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7162 (mmt90)
REVERT: R    6 GLN cc_start: 0.8334 (mp10) cc_final: 0.8060 (mt0)
REVERT: R   53 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8579 (tp)
REVERT: R  135 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8065 (mm)
REVERT: R  137 HIS cc_start: 0.7700 (m-70) cc_final: 0.6839 (m-70)
REVERT: R  188 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8866 (mp)
REVERT: R  259 LYS cc_start: 0.8988 (mtpt) cc_final: 0.8653 (mtpp)
  outliers start: 29
  outliers final: 15
  residues processed: 169
  average time/residue: 1.1699
  time to fit residues: 210.7919
Evaluate side-chains
  163 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ARG
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue   98 ARG
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   79 CYS
Chi-restraints excluded: chain R residue  133 LEU
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  188 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0470
   chunk 63 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 39 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0370
   chunk 69 optimal weight:    0.8980
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.5956

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN
B 155 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  23 ASN
R 244 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.135692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.100747 restraints weight = 13405.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.50
r_work: 0.3190 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8766  Z= 0.109
  Angle     :  0.567   9.091  11908  Z= 0.289
  Chirality :  0.042   0.159   1349
  Planarity :  0.004   0.058   1523
  Dihedral  :  4.176  45.119   1218
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.73 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.26), residues: 1101
  helix:  2.62 (0.27), residues: 377
  sheet:  1.01 (0.32), residues: 258
  loop :  0.21 (0.31), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.015   0.001   TYR E 190 
 ARG   0.013   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03201 (  450)
  hydrogen bonds       : angle       4.13131 ( 1284)
  SS BOND              : bond        0.00449 (    1)
  SS BOND              : angle       0.57641 (    2)
  covalent geometry    : bond        0.00243 ( 8765)
  covalent geometry    : angle       0.56744 (11906)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 153
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 ASP cc_start: 0.8697 (m-30) cc_final: 0.8448 (m-30)
REVERT: C   32 LYS cc_start: 0.8503 (tppt) cc_final: 0.8189 (tppt)
REVERT: E   46 GLU cc_start: 0.8480 (tt0) cc_final: 0.8230 (pt0)
REVERT: E   87 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7193 (mmt90)
REVERT: R  135 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8029 (mm)
REVERT: R  137 HIS cc_start: 0.7693 (m-70) cc_final: 0.6775 (m-70)
REVERT: R  188 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8875 (mp)
REVERT: R  259 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8641 (mtpp)
  outliers start: 27
  outliers final: 13
  residues processed: 172
  average time/residue: 1.1224
  time to fit residues: 206.0628
Evaluate side-chains
  164 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ARG
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue   98 ARG
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue   79 CYS
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  188 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 106 optimal weight:    6.9990
   chunk 99 optimal weight:    0.2980
   chunk 102 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 100 optimal weight:    0.8980
   chunk 42 optimal weight:    8.9990
   chunk 108 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN
B 155 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  82 GLN
R 244 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.133638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.098418 restraints weight = 13352.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.50
r_work: 0.3156 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8766  Z= 0.139
  Angle     :  0.613   8.289  11908  Z= 0.313
  Chirality :  0.043   0.173   1349
  Planarity :  0.004   0.058   1523
  Dihedral  :  4.340  42.581   1218
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 20.73 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.26), residues: 1101
  helix:  2.53 (0.27), residues: 378
  sheet:  0.90 (0.32), residues: 262
  loop :  0.28 (0.31), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 339 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.012   0.001   PHE E 212 
 TYR   0.020   0.001   TYR E 190 
 ARG   0.013   0.001   ARG A 161 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03523 (  450)
  hydrogen bonds       : angle       4.22095 ( 1284)
  SS BOND              : bond        0.00466 (    1)
  SS BOND              : angle       0.72073 (    2)
  covalent geometry    : bond        0.00322 ( 8765)
  covalent geometry    : angle       0.61250 (11906)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 0.882 
Fit side-chains
REVERT: B  260 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8298 (tm-30)
REVERT: E   46 GLU cc_start: 0.8496 (tt0) cc_final: 0.8267 (pt0)
REVERT: E   87 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7191 (mmt90)
REVERT: E  220 GLU cc_start: 0.6813 (mp0) cc_final: 0.6588 (mp0)
REVERT: R    6 GLN cc_start: 0.8567 (mp10) cc_final: 0.8156 (mt0)
REVERT: R  135 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8063 (mm)
REVERT: R  137 HIS cc_start: 0.7675 (m-70) cc_final: 0.6811 (m-70)
REVERT: R  188 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8877 (mp)
REVERT: R  259 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8696 (mtpp)
  outliers start: 23
  outliers final: 13
  residues processed: 163
  average time/residue: 1.1893
  time to fit residues: 206.2661
Evaluate side-chains
  160 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ARG
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue   98 ARG
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue   79 CYS
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  188 LEU
Chi-restraints excluded: chain R residue  270 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 81 optimal weight:    0.6980
   chunk 83 optimal weight:    6.9990
   chunk 100 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN
B 155 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 244 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.133866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.098691 restraints weight = 13368.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.50
r_work: 0.3162 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8766  Z= 0.132
  Angle     :  0.605   8.163  11908  Z= 0.310
  Chirality :  0.043   0.166   1349
  Planarity :  0.004   0.058   1523
  Dihedral  :  4.333  38.987   1218
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 21.84 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.26), residues: 1101
  helix:  2.45 (0.27), residues: 378
  sheet:  1.01 (0.31), residues: 258
  loop :  0.25 (0.31), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 339 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.020   0.001   TYR E 190 
 ARG   0.010   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03503 (  450)
  hydrogen bonds       : angle       4.25963 ( 1284)
  SS BOND              : bond        0.00510 (    1)
  SS BOND              : angle       0.64636 (    2)
  covalent geometry    : bond        0.00304 ( 8765)
  covalent geometry    : angle       0.60500 (11906)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
REVERT: B  260 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8241 (tm-30)
REVERT: E   46 GLU cc_start: 0.8519 (tt0) cc_final: 0.8289 (pt0)
REVERT: E   87 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7148 (mmt90)
REVERT: R    6 GLN cc_start: 0.8536 (mp10) cc_final: 0.8190 (mt0)
REVERT: R  135 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8037 (mm)
REVERT: R  137 HIS cc_start: 0.7644 (m-70) cc_final: 0.6775 (m-70)
REVERT: R  188 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8874 (mp)
REVERT: R  259 LYS cc_start: 0.9018 (mtpt) cc_final: 0.8687 (mtpp)
  outliers start: 21
  outliers final: 16
  residues processed: 158
  average time/residue: 1.1370
  time to fit residues: 191.6496
Evaluate side-chains
  163 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ARG
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue   98 ARG
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue   79 CYS
Chi-restraints excluded: chain R residue  133 LEU
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  188 LEU
Chi-restraints excluded: chain R residue  270 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 69 optimal weight:    7.9990
   chunk 23 optimal weight:    0.3980
   chunk 15 optimal weight:    6.9990
   chunk 64 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 89 optimal weight:    6.9990
   chunk 106 optimal weight:    6.9990
   chunk 98 optimal weight:    7.9990
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN
B 155 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  82 GLN
R 244 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.130806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.095157 restraints weight = 13375.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.49
r_work: 0.3104 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8766  Z= 0.205
  Angle     :  0.665   8.219  11908  Z= 0.345
  Chirality :  0.046   0.191   1349
  Planarity :  0.004   0.059   1523
  Dihedral  :  4.827  48.939   1218
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 21.62 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.26), residues: 1101
  helix:  2.31 (0.27), residues: 378
  sheet:  0.77 (0.31), residues: 270
  loop :  0.26 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 131 
 HIS   0.006   0.001   HIS E  35 
 PHE   0.015   0.002   PHE B 253 
 TYR   0.025   0.002   TYR E 190 
 ARG   0.022   0.001   ARG A 161 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04100 (  450)
  hydrogen bonds       : angle       4.46882 ( 1284)
  SS BOND              : bond        0.00561 (    1)
  SS BOND              : angle       0.86115 (    2)
  covalent geometry    : bond        0.00476 ( 8765)
  covalent geometry    : angle       0.66540 (11906)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8011.12 seconds
wall clock time: 138 minutes 6.69 seconds (8286.69 seconds total)