Starting phenix.real_space_refine
on Sun May 11 01:37:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9l3w_62793/05_2025/9l3w_62793.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9l3w_62793/05_2025/9l3w_62793.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9l3w_62793/05_2025/9l3w_62793.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9l3w_62793/05_2025/9l3w_62793.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9l3w_62793/05_2025/9l3w_62793.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9l3w_62793/05_2025/9l3w_62793.cif"
  }
  resolution = 3.5
  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=   0.016 sd=   0.071
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      60      5.16       5
     C    4651      2.51       5
     N    1229      2.21       5
     O    1322      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7262
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1572
          Classifications: {'peptide': 205}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 1, 'TRANS': 203}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 94
          Unresolved non-hydrogen angles: 107
          Unresolved non-hydrogen dihedrals: 81
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 45
    Chain: "B"
      Number of atoms: 2487
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2487
          Classifications: {'peptide': 335}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 5, 'TRANS': 329}
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 107
          Unresolved non-hydrogen dihedrals: 71
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 69
    Chain: "C"
      Number of atoms: 353
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 353
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 78
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "L"
      Number of atoms: 732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 732
          Classifications: {'peptide': 108}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 4, 'TRANS': 103}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 148
          Unresolved non-hydrogen angles: 177
          Unresolved non-hydrogen dihedrals: 130
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 10, 'PHE:plan': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 107
    Chain: "R"
      Number of atoms: 2118
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2118
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 10, 'TRANS': 270}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 127
          Unresolved non-hydrogen angles: 159
          Unresolved non-hydrogen dihedrals: 103
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 61
  Time building chain proxies: 4.87, per 1000 atoms: 0.67
  Number of scatterers: 7262
  At special positions: 0
  Unit cell: (76.041, 100.674, 163.863, 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      60     16.00
     O    1322      8.00
     N    1229      7.00
     C    4651      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  47 " - pdb=" SG  CYS A 224 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  77 " - pdb=" SG  CYS L  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  98 " - pdb=" SG  CYS L 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 101 " - pdb=" SG  CYS L 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 112 " - pdb=" SG  CYS R 189 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.83
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1866

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      42.4% alpha, 17.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 31
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.733A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.705A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.717A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
      removed outlier: 4.036A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 3.549A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 7 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 10 through 23
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.575A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 3.585A  pdb=" N   ASP C  48 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 48'
    Processing helix  chain 'L' and resid 23 through 35
      removed outlier: 3.523A  pdb=" N   VAL L  32 " --> pdb=" O   ARG L  28 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 4.149A  pdb=" N   LYS L  83 " --> pdb=" O   ARG L  80 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LYS L  84 " --> pdb=" O   ASP L  81 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 80 through 84'
    Processing helix  chain 'L' and resid 132 through 137
      removed outlier: 3.883A  pdb=" N   LEU L 136 " --> pdb=" O   GLU L 132 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   ARG L 137 " --> pdb=" O   THR L 133 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 132 through 137'
    Processing helix  chain 'L' and resid 144 through 148
    Processing helix  chain 'R' and resid 37 through 67
      removed outlier: 3.808A  pdb=" N   VAL R  45 " --> pdb=" O   ILE R  41 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   VAL R  46 " --> pdb=" O   PHE R  42 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 72 through 101
      Proline residue:  R  93  - end of helix
    Processing helix  chain 'R' and resid 111 through 143
      removed outlier: 4.408A  pdb=" N   PHE R 117 " --> pdb=" O   LYS R 113 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 143 through 150
    Processing helix  chain 'R' and resid 152 through 177
      Proline residue:  R 173  - end of helix
      removed outlier: 3.806A  pdb=" N   VAL R 176 " --> pdb=" O   SER R 172 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 220 through 250
      removed outlier: 5.569A  pdb=" N   VAL R 231 " --> pdb=" O   CYS R 227 " (cutoff:3.500A)
      Proline residue:  R 232  - end of helix
      removed outlier: 3.913A  pdb=" N   ASN R 250 " --> pdb=" O   LYS R 246 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 256 through 283
      removed outlier: 3.743A  pdb=" N   LYS R 260 " --> pdb=" O   LYS R 256 " (cutoff:3.500A)
      Proline residue:  R 275  - end of helix
    Processing helix  chain 'R' and resid 290 through 317
      removed outlier: 4.153A  pdb=" N   PHE R 294 " --> pdb=" O   PRO R 290 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   LEU R 298 " --> pdb=" O   PHE R 294 " (cutoff:3.500A)
      Proline residue:  R 299  - end of helix
      removed outlier: 3.666A  pdb=" N   ASN R 308 " --> pdb=" O   LEU R 304 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   SER R 309 " --> pdb=" O   ALA R 305 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   CYS R 310 " --> pdb=" O   ILE R 306 " (cutoff:3.500A)
      Proline residue:  R 313  - end of helix
    Processing helix  chain 'R' and resid 320 through 330
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.258A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.738A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.501A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.347A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.570A  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: 5.724A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.836A  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: 3.686A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.092A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.238A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.984A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.660A  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: 3.871A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.486A  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: 3.639A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.983A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 45 through 48
      removed outlier: 5.963A  pdb=" N   ALA L  46 " --> pdb=" O   THR L  75 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   THR L  75 " --> pdb=" O   ALA L  46 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   GLN L  48 " --> pdb=" O   GLN L  73 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   GLN L  73 " --> pdb=" O   GLN L  48 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'R' and resid 179 through 181

    378 hydrogen bonds defined for protein.
    1080 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: 2.01

  Time building geometry restraints manager: 2.17 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2337
        1.35 -     1.46: 1820
        1.46 -     1.58: 3167
        1.58 -     1.70: 0
        1.70 -     1.82: 81
  Bond restraints: 7405
  Sorted by residual:
  bond pdb=" CA  VAL L  89 "
       pdb=" CB  VAL L  89 "
    ideal  model  delta    sigma   weight residual
    1.540  1.566 -0.026 2.70e-02 1.37e+03 9.52e-01
  bond pdb=" N   ASN B 119 "
       pdb=" CA  ASN B 119 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 9.47e-01
  bond pdb=" CA  ILE B  43 "
       pdb=" CB  ILE B  43 "
    ideal  model  delta    sigma   weight residual
    1.530  1.540 -0.010 1.11e-02 8.12e+03 7.85e-01
  bond pdb=" C   LEU R  92 "
       pdb=" N   PRO R  93 "
    ideal  model  delta    sigma   weight residual
    1.335  1.345 -0.010 1.28e-02 6.10e+03 6.11e-01
  bond pdb=" CB  PRO A 282 "
       pdb=" CG  PRO A 282 "
    ideal  model  delta    sigma   weight residual
    1.492  1.531 -0.039 5.00e-02 4.00e+02 6.09e-01
  ... (remaining 7400 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 9928
        1.69 -     3.38: 117
        3.38 -     5.07: 26
        5.07 -     6.77: 3
        6.77 -     8.46: 1
  Bond angle restraints: 10075
  Sorted by residual:
  angle pdb=" C   PHE R  91 "
        pdb=" N   LEU R  92 "
        pdb=" CA  LEU R  92 "
      ideal   model   delta    sigma   weight residual
     120.09  123.64   -3.55 1.25e+00 6.40e-01 8.04e+00
  angle pdb=" CB  MET B 325 "
        pdb=" CG  MET B 325 "
        pdb=" SD  MET B 325 "
      ideal   model   delta    sigma   weight residual
     112.70  121.16   -8.46 3.00e+00 1.11e-01 7.95e+00
  angle pdb=" C   CYS R  51 "
        pdb=" N   PHE R  52 "
        pdb=" CA  PHE R  52 "
      ideal   model   delta    sigma   weight residual
     120.68  116.29    4.39 1.70e+00 3.46e-01 6.68e+00
  angle pdb=" N   PHE L 154 "
        pdb=" CA  PHE L 154 "
        pdb=" C   PHE L 154 "
      ideal   model   delta    sigma   weight residual
     111.81  108.19    3.62 1.44e+00 4.82e-01 6.32e+00
  angle pdb=" N   PHE R  52 "
        pdb=" CA  PHE R  52 "
        pdb=" CB  PHE R  52 "
      ideal   model   delta    sigma   weight residual
     110.30  114.07   -3.77 1.54e+00 4.22e-01 6.00e+00
  ... (remaining 10070 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 3968
       17.37 -    34.74: 305
       34.74 -    52.12: 64
       52.12 -    69.49: 4
       69.49 -    86.86: 5
  Dihedral angle restraints: 4346
    sinusoidal: 1489
      harmonic: 2857
  Sorted by residual:
  dihedral pdb=" CB  CYS L  77 "
           pdb=" SG  CYS L  77 "
           pdb=" SG  CYS L  87 "
           pdb=" CB  CYS L  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    0.86  -86.86     1      1.00e+01 1.00e-02 9.07e+01
  dihedral pdb=" CB  CYS R 112 "
           pdb=" SG  CYS R 112 "
           pdb=" SG  CYS R 189 "
           pdb=" CB  CYS R 189 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  148.82  -55.82     1      1.00e+01 1.00e-02 4.21e+01
  dihedral pdb=" CA  ASN R 191 "
           pdb=" C   ASN R 191 "
           pdb=" N   ASN R 192 "
           pdb=" CA  ASN R 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.18  -18.82     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 4343 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 687
       0.027 -    0.055: 346
       0.055 -    0.082: 110
       0.082 -    0.110: 49
       0.110 -    0.137: 15
  Chirality restraints: 1207
  Sorted by residual:
  chirality pdb=" CA  VAL B 296 "
            pdb=" N   VAL B 296 "
            pdb=" C   VAL B 296 "
            pdb=" CB  VAL B 296 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.71e-01
  chirality pdb=" CA  ILE B 123 "
            pdb=" N   ILE B 123 "
            pdb=" C   ILE B 123 "
            pdb=" CB  ILE B 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.15e-01
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.09e-01
  ... (remaining 1204 not shown)

  Planarity restraints: 1265
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER R 172 "    0.021 5.00e-02 4.00e+02   3.23e-02 1.66e+00
        pdb=" N   PRO R 173 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO R 173 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO R 173 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 175 "    0.006 2.00e-02 2.50e+03   1.28e-02 1.63e+00
        pdb=" CD  GLN B 175 "   -0.022 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 175 "    0.008 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 175 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.021 5.00e-02 4.00e+02   3.16e-02 1.60e+00
        pdb=" N   PRO B 236 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1262 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 97
        2.68 -     3.23: 6900
        3.23 -     3.79: 11223
        3.79 -     4.34: 15098
        4.34 -     4.90: 24807
  Nonbonded interactions: 58125
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.121 3.040
  nonbonded pdb=" OG1 THR B  29 "
            pdb=" OE1 GLN B  32 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   CYS A 254 "
            pdb=" NZ  LYS A 317 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" ND2 ASN B 230 "
            pdb=" OD1 ASP B 246 "
     model   vdw
     2.304 3.120
  ... (remaining 58120 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.160
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
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      :  0.002   0.039   7410  Z= 0.102
  Angle     :  0.515   8.458  10085  Z= 0.288
  Chirality :  0.039   0.137   1207
  Planarity :  0.003   0.032   1265
  Dihedral  : 12.785  70.417   2465
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.28), residues: 953
  helix:  2.09 (0.28), residues: 388
  sheet:  0.09 (0.36), residues: 192
  loop : -1.06 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS L 146 
 PHE   0.010   0.001   PHE A 196 
 TYR   0.021   0.001   TYR R  47 
 ARG   0.003   0.000   ARG R 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14320 (  378)
  hydrogen bonds       : angle       5.24384 ( 1080)
  SS BOND              : bond        0.00190 (    5)
  SS BOND              : angle       0.34290 (   10)
  covalent geometry    : bond        0.00195 ( 7405)
  covalent geometry    : angle       0.51492 (10075)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.749 
Fit side-chains
REVERT: L   64 ILE cc_start: 0.7541 (mp) cc_final: 0.7133 (tp)
REVERT: R   61 VAL cc_start: 0.9050 (p) cc_final: 0.8841 (t)
REVERT: R  132 ILE cc_start: 0.8021 (tp) cc_final: 0.7749 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1673
  time to fit residues: 26.8460
Evaluate side-chains
  99 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 75 optimal weight:    0.8980
   chunk 29 optimal weight:    6.9990
   chunk 45 optimal weight:    0.2980
   chunk 56 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
L 153 GLN
R 286 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.102528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.087663 restraints weight = 17665.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.086572 restraints weight = 23581.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.084908 restraints weight = 19096.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7410  Z= 0.168
  Angle     :  0.579   7.960  10085  Z= 0.305
  Chirality :  0.043   0.144   1207
  Planarity :  0.004   0.034   1265
  Dihedral  :  3.877  23.818   1022
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  9.08 %
    Favored  : 89.27 %
  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:  0.65 (0.28), residues: 953
  helix:  1.85 (0.27), residues: 391
  sheet:  0.44 (0.37), residues: 178
  loop : -1.07 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 211 
 HIS   0.005   0.001   HIS B  91 
 PHE   0.020   0.002   PHE B 292 
 TYR   0.018   0.002   TYR R  47 
 ARG   0.007   0.001   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04180 (  378)
  hydrogen bonds       : angle       4.29927 ( 1080)
  SS BOND              : bond        0.00406 (    5)
  SS BOND              : angle       0.56418 (   10)
  covalent geometry    : bond        0.00393 ( 7405)
  covalent geometry    : angle       0.57949 (10075)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.866 
Fit side-chains
REVERT: B  256 ARG cc_start: 0.7590 (mtm180) cc_final: 0.7104 (mtp180)
REVERT: B  262 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7303 (ttt)
REVERT: R   61 VAL cc_start: 0.8784 (p) cc_final: 0.8515 (t)
  outliers start: 12
  outliers final: 9
  residues processed: 107
  average time/residue: 0.1787
  time to fit residues: 26.5248
Evaluate side-chains
  105 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain L residue  153 GLN
Chi-restraints excluded: chain R residue   52 PHE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  219 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 66 optimal weight:    8.9990
   chunk 50 optimal weight:    5.9990
   chunk 28 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 65 optimal weight:    8.9990
   chunk 87 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 23 optimal weight:    0.1980
   chunk 19 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 62 optimal weight:    9.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.102793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.087166 restraints weight = 18083.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.088154 restraints weight = 28656.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.089301 restraints weight = 19956.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7410  Z= 0.118
  Angle     :  0.515   7.359  10085  Z= 0.273
  Chirality :  0.041   0.136   1207
  Planarity :  0.003   0.035   1265
  Dihedral  :  3.809  23.358   1022
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.79 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.28), residues: 953
  helix:  1.81 (0.27), residues: 392
  sheet:  0.34 (0.36), residues: 178
  loop : -1.08 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.015   0.001   PHE L 154 
 TYR   0.018   0.002   TYR A 302 
 ARG   0.003   0.000   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03701 (  378)
  hydrogen bonds       : angle       4.14657 ( 1080)
  SS BOND              : bond        0.00379 (    5)
  SS BOND              : angle       0.34781 (   10)
  covalent geometry    : bond        0.00264 ( 7405)
  covalent geometry    : angle       0.51531 (10075)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.786 
Fit side-chains
REVERT: B  256 ARG cc_start: 0.7595 (mtm180) cc_final: 0.6952 (mtm180)
REVERT: B  262 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7016 (ttm)
REVERT: C   50 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6920 (mp)
REVERT: R   61 VAL cc_start: 0.8727 (p) cc_final: 0.8480 (t)
  outliers start: 13
  outliers final: 10
  residues processed: 104
  average time/residue: 0.1762
  time to fit residues: 25.2371
Evaluate side-chains
  111 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain R residue   64 ILE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  139 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0980
   chunk 22 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 75 optimal weight:    0.1980
   chunk 85 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.102691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.087404 restraints weight = 18041.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.089255 restraints weight = 30632.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.090159 restraints weight = 17901.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7410  Z= 0.110
  Angle     :  0.498   6.532  10085  Z= 0.263
  Chirality :  0.040   0.135   1207
  Planarity :  0.003   0.035   1265
  Dihedral  :  3.754  23.269   1022
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 13.76 %
    Favored  : 83.49 %
  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:  0.58 (0.28), residues: 953
  helix:  1.87 (0.27), residues: 392
  sheet:  0.23 (0.36), residues: 179
  loop : -1.13 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R  77 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.014   0.001   PHE A 196 
 TYR   0.013   0.001   TYR R  47 
 ARG   0.003   0.000   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03445 (  378)
  hydrogen bonds       : angle       4.05472 ( 1080)
  SS BOND              : bond        0.00357 (    5)
  SS BOND              : angle       0.33647 (   10)
  covalent geometry    : bond        0.00244 ( 7405)
  covalent geometry    : angle       0.49843 (10075)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.770 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6923 (mtp-110)
REVERT: B  256 ARG cc_start: 0.7607 (mtm180) cc_final: 0.6937 (mtm180)
REVERT: B  262 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.6725 (tpp)
REVERT: C   50 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6987 (mp)
REVERT: R   61 VAL cc_start: 0.8713 (p) cc_final: 0.8483 (t)
  outliers start: 20
  outliers final: 16
  residues processed: 111
  average time/residue: 0.1841
  time to fit residues: 27.7543
Evaluate side-chains
  117 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain R residue   64 ILE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  139 ILE
Chi-restraints excluded: chain R residue  233 VAL
Chi-restraints excluded: chain R residue  243 ILE
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 85 optimal weight:    0.0970
   chunk 77 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 286 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.102050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.086806 restraints weight = 17644.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.088332 restraints weight = 29517.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.088915 restraints weight = 20691.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7410  Z= 0.119
  Angle     :  0.514   6.742  10085  Z= 0.269
  Chirality :  0.041   0.148   1207
  Planarity :  0.003   0.036   1265
  Dihedral  :  3.800  23.958   1022
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 14.58 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.28), residues: 953
  helix:  1.84 (0.27), residues: 392
  sheet:  0.18 (0.36), residues: 185
  loop : -1.11 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 211 
 HIS   0.008   0.001   HIS R 286 
 PHE   0.014   0.001   PHE R  52 
 TYR   0.012   0.001   TYR R  47 
 ARG   0.003   0.000   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03504 (  378)
  hydrogen bonds       : angle       4.05782 ( 1080)
  SS BOND              : bond        0.00375 (    5)
  SS BOND              : angle       0.42690 (   10)
  covalent geometry    : bond        0.00269 ( 7405)
  covalent geometry    : angle       0.51375 (10075)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.822 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6901 (mtp-110)
REVERT: B  256 ARG cc_start: 0.7605 (mtm180) cc_final: 0.6976 (mtm180)
REVERT: B  262 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.6626 (tpp)
REVERT: C   50 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.7019 (mp)
REVERT: R   61 VAL cc_start: 0.8681 (p) cc_final: 0.8428 (t)
REVERT: R   79 LEU cc_start: 0.8318 (tp) cc_final: 0.8102 (tp)
  outliers start: 25
  outliers final: 20
  residues processed: 114
  average time/residue: 0.1898
  time to fit residues: 29.6074
Evaluate side-chains
  122 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain R residue   52 PHE
Chi-restraints excluded: chain R residue   64 ILE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  106 VAL
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  139 ILE
Chi-restraints excluded: chain R residue  233 VAL
Chi-restraints excluded: chain R residue  243 ILE
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 66 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 71 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 91 optimal weight:    0.0770
   chunk 50 optimal weight:    0.9980
   overall best weight:    1.2144

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B 175 GLN
** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 286 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.100335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 105)---------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.081567 restraints weight = 17822.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.081036 restraints weight = 20583.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.081787 restraints weight = 18315.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7410  Z= 0.166
  Angle     :  0.577   8.107  10085  Z= 0.301
  Chirality :  0.043   0.151   1207
  Planarity :  0.004   0.035   1265
  Dihedral  :  4.156  27.882   1022
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 14.99 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.28), residues: 953
  helix:  1.65 (0.27), residues: 394
  sheet:  0.36 (0.36), residues: 189
  loop : -1.22 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 211 
 HIS   0.007   0.001   HIS R 286 
 PHE   0.014   0.002   PHE R  52 
 TYR   0.014   0.002   TYR R  47 
 ARG   0.005   0.001   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04022 (  378)
  hydrogen bonds       : angle       4.30372 ( 1080)
  SS BOND              : bond        0.00559 (    5)
  SS BOND              : angle       0.72338 (   10)
  covalent geometry    : bond        0.00390 ( 7405)
  covalent geometry    : angle       0.57634 (10075)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 98
  time to evaluate  : 0.748 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.6870 (mtp-110)
REVERT: B  256 ARG cc_start: 0.7500 (mtm180) cc_final: 0.6890 (mtm180)
REVERT: B  262 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.6648 (tpp)
REVERT: R   61 VAL cc_start: 0.8821 (p) cc_final: 0.8570 (t)
REVERT: R  101 MET cc_start: 0.8320 (mtp) cc_final: 0.8057 (mtm)
  outliers start: 28
  outliers final: 21
  residues processed: 114
  average time/residue: 0.1892
  time to fit residues: 29.1841
Evaluate side-chains
  118 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain R residue   52 PHE
Chi-restraints excluded: chain R residue   64 ILE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  106 VAL
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  139 ILE
Chi-restraints excluded: chain R residue  219 VAL
Chi-restraints excluded: chain R residue  233 VAL
Chi-restraints excluded: chain R residue  243 ILE
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 67 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 40 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B  44 GLN
B 175 GLN
B 239 ASN
** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 286 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.100972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.085615 restraints weight = 17709.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.083950 restraints weight = 22153.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.082534 restraints weight = 18075.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7410  Z= 0.128
  Angle     :  0.530   6.847  10085  Z= 0.278
  Chirality :  0.041   0.143   1207
  Planarity :  0.003   0.035   1265
  Dihedral  :  4.025  26.563   1022
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.23 %
    Favored  : 80.61 %
  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:  0.48 (0.28), residues: 953
  helix:  1.71 (0.27), residues: 394
  sheet:  0.29 (0.36), residues: 183
  loop : -1.18 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 211 
 HIS   0.008   0.001   HIS R 286 
 PHE   0.013   0.001   PHE R  52 
 TYR   0.012   0.001   TYR R  47 
 ARG   0.004   0.000   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03634 (  378)
  hydrogen bonds       : angle       4.13153 ( 1080)
  SS BOND              : bond        0.00439 (    5)
  SS BOND              : angle       0.47204 (   10)
  covalent geometry    : bond        0.00293 ( 7405)
  covalent geometry    : angle       0.52981 (10075)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.854 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6912 (mtp-110)
REVERT: B  256 ARG cc_start: 0.7491 (mtm180) cc_final: 0.6884 (mtm180)
REVERT: B  262 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.6603 (tpp)
REVERT: R   61 VAL cc_start: 0.8829 (p) cc_final: 0.8598 (t)
REVERT: R  101 MET cc_start: 0.8309 (mtp) cc_final: 0.8024 (mtm)
  outliers start: 23
  outliers final: 18
  residues processed: 108
  average time/residue: 0.1990
  time to fit residues: 29.1932
Evaluate side-chains
  114 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 1.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain R residue   52 PHE
Chi-restraints excluded: chain R residue   64 ILE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  106 VAL
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  139 ILE
Chi-restraints excluded: chain R residue  233 VAL
Chi-restraints excluded: chain R residue  243 ILE
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 65 optimal weight:   20.0000
   chunk 1 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 57 optimal weight:    7.9990
   chunk 7 optimal weight:    0.7980
   chunk 53 optimal weight:   30.0000
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 286 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.100333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.084929 restraints weight = 17886.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.085607 restraints weight = 27897.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.086353 restraints weight = 24815.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7410  Z= 0.148
  Angle     :  0.554   7.367  10085  Z= 0.290
  Chirality :  0.042   0.146   1207
  Planarity :  0.004   0.034   1265
  Dihedral  :  4.131  27.956   1022
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 16.23 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.28), residues: 953
  helix:  1.65 (0.27), residues: 396
  sheet:  0.30 (0.37), residues: 182
  loop : -1.15 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 211 
 HIS   0.008   0.001   HIS R 286 
 PHE   0.014   0.001   PHE A 196 
 TYR   0.014   0.002   TYR R  47 
 ARG   0.005   0.000   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03838 (  378)
  hydrogen bonds       : angle       4.19616 ( 1080)
  SS BOND              : bond        0.00494 (    5)
  SS BOND              : angle       0.62521 (   10)
  covalent geometry    : bond        0.00348 ( 7405)
  covalent geometry    : angle       0.55408 (10075)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.805 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6760 (mtp-110)
REVERT: B  256 ARG cc_start: 0.7506 (mtm180) cc_final: 0.6900 (mtm180)
REVERT: B  262 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6613 (tpp)
REVERT: R   61 VAL cc_start: 0.8728 (p) cc_final: 0.8488 (t)
REVERT: R  101 MET cc_start: 0.8332 (mtp) cc_final: 0.8072 (mtm)
  outliers start: 26
  outliers final: 22
  residues processed: 109
  average time/residue: 0.2052
  time to fit residues: 29.7848
Evaluate side-chains
  117 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain R residue   52 PHE
Chi-restraints excluded: chain R residue   64 ILE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  106 VAL
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  139 ILE
Chi-restraints excluded: chain R residue  219 VAL
Chi-restraints excluded: chain R residue  233 VAL
Chi-restraints excluded: chain R residue  243 ILE
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 59 optimal weight:    0.0770
   chunk 89 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 53 optimal weight:   30.0000
   chunk 27 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.6740

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 286 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.101065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.085791 restraints weight = 17948.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.083650 restraints weight = 22431.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.081442 restraints weight = 20096.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7410  Z= 0.116
  Angle     :  0.518   7.200  10085  Z= 0.272
  Chirality :  0.041   0.144   1207
  Planarity :  0.003   0.034   1265
  Dihedral  :  3.991  26.333   1022
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.33 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.28), residues: 953
  helix:  1.85 (0.27), residues: 388
  sheet:  0.26 (0.36), residues: 182
  loop : -1.15 (0.33), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 211 
 HIS   0.008   0.001   HIS R 286 
 PHE   0.013   0.001   PHE R  52 
 TYR   0.012   0.001   TYR R  47 
 ARG   0.004   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03473 (  378)
  hydrogen bonds       : angle       4.05907 ( 1080)
  SS BOND              : bond        0.00396 (    5)
  SS BOND              : angle       0.48290 (   10)
  covalent geometry    : bond        0.00262 ( 7405)
  covalent geometry    : angle       0.51831 (10075)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7110 (mtp-110)
REVERT: B   44 GLN cc_start: 0.6910 (tp-100) cc_final: 0.6654 (tp-100)
REVERT: B  256 ARG cc_start: 0.7454 (mtm180) cc_final: 0.6859 (mtm180)
REVERT: B  262 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.6542 (tpp)
REVERT: R   61 VAL cc_start: 0.8871 (p) cc_final: 0.8653 (t)
REVERT: R  101 MET cc_start: 0.8277 (mtp) cc_final: 0.8021 (mtm)
  outliers start: 20
  outliers final: 18
  residues processed: 106
  average time/residue: 0.1946
  time to fit residues: 27.6454
Evaluate side-chains
  112 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain R residue   52 PHE
Chi-restraints excluded: chain R residue   64 ILE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  106 VAL
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  139 ILE
Chi-restraints excluded: chain R residue  233 VAL
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 78 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 82 optimal weight:    5.9990
   chunk 92 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 286 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.100753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.085562 restraints weight = 18142.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.086837 restraints weight = 31369.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.088087 restraints weight = 19531.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7410  Z= 0.128
  Angle     :  0.531   7.085  10085  Z= 0.278
  Chirality :  0.041   0.145   1207
  Planarity :  0.003   0.034   1265
  Dihedral  :  4.017  26.914   1022
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.19 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.28), residues: 953
  helix:  1.82 (0.27), residues: 390
  sheet:  0.27 (0.36), residues: 182
  loop : -1.14 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 211 
 HIS   0.008   0.001   HIS R 286 
 PHE   0.013   0.001   PHE R  52 
 TYR   0.013   0.001   TYR R  47 
 ARG   0.005   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03582 (  378)
  hydrogen bonds       : angle       4.09897 ( 1080)
  SS BOND              : bond        0.00422 (    5)
  SS BOND              : angle       0.55750 (   10)
  covalent geometry    : bond        0.00294 ( 7405)
  covalent geometry    : angle       0.53065 (10075)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.771 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6812 (mtp-110)
REVERT: B  256 ARG cc_start: 0.7495 (mtm180) cc_final: 0.6880 (mtm180)
REVERT: B  262 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6547 (tpp)
REVERT: R   61 VAL cc_start: 0.8709 (p) cc_final: 0.8473 (t)
REVERT: R  101 MET cc_start: 0.8297 (mtp) cc_final: 0.8049 (mtm)
  outliers start: 21
  outliers final: 18
  residues processed: 105
  average time/residue: 0.2005
  time to fit residues: 28.1437
Evaluate side-chains
  112 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain R residue   52 PHE
Chi-restraints excluded: chain R residue   64 ILE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  106 VAL
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  139 ILE
Chi-restraints excluded: chain R residue  233 VAL
Chi-restraints excluded: chain R residue  243 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0670
   chunk 9 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 53 optimal weight:   30.0000
   chunk 43 optimal weight:    0.7980
   chunk 16 optimal weight:    0.3980
   chunk 65 optimal weight:   10.0000
   chunk 61 optimal weight:    7.9990
   overall best weight:    0.6520

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 286 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.101181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.086031 restraints weight = 17809.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.086771 restraints weight = 26735.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.087682 restraints weight = 22165.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7410  Z= 0.115
  Angle     :  0.520   7.078  10085  Z= 0.273
  Chirality :  0.041   0.144   1207
  Planarity :  0.003   0.034   1265
  Dihedral  :  3.965  25.898   1022
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.19 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.28), residues: 953
  helix:  1.88 (0.27), residues: 388
  sheet:  0.17 (0.37), residues: 184
  loop : -1.16 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R  77 
 HIS   0.008   0.001   HIS R 286 
 PHE   0.013   0.001   PHE R  52 
 TYR   0.012   0.001   TYR R  47 
 ARG   0.007   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03427 (  378)
  hydrogen bonds       : angle       4.03561 ( 1080)
  SS BOND              : bond        0.00380 (    5)
  SS BOND              : angle       0.49005 (   10)
  covalent geometry    : bond        0.00259 ( 7405)
  covalent geometry    : angle       0.51968 (10075)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2469.50 seconds
wall clock time: 44 minutes 17.31 seconds (2657.31 seconds total)