Starting phenix.real_space_refine
on Fri Mar 14 06:04:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rxc_24728/03_2025/7rxc_24728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rxc_24728/03_2025/7rxc_24728.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rxc_24728/03_2025/7rxc_24728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rxc_24728/03_2025/7rxc_24728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rxc_24728/03_2025/7rxc_24728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rxc_24728/03_2025/7rxc_24728.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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      32      5.16       5
     C    6056      2.51       5
     N    1510      2.21       5
     O    1762      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9360
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "H"
      Number of atoms: 1582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1582
          Classifications: {'peptide': 207}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 192}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 1588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1588
          Classifications: {'peptide': 204}
          Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 194}
          Chain breaks: 2
    Chain: "N"
      Number of atoms: 1008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 1008
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 3, 'TRANS': 122}
    Chain: "B"
      Number of atoms: 3433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 3433
          Classifications: {'peptide': 439}
          Link IDs: {'PTRANS': 24, 'TRANS': 414}
          Chain breaks: 4
    Chain: "K"
      Number of atoms: 1661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1661
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 3, 'TRANS': 198}
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'GLC': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "K"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 65
          Unusual residues: {'POV': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 143
          Unresolved non-hydrogen angles: 179
          Unresolved non-hydrogen dihedrals: 123
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 4}
          Unresolved non-hydrogen planarities: 23
  Time building chain proxies: 5.29, per 1000 atoms: 0.57
  Number of scatterers: 9360
  At special positions: 0
  Unit cell: (128.26, 125.08, 108.12, 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      32     16.00
     O    1762      8.00
     N    1510      7.00
     C    6056      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 150 " - pdb=" SG  CYS H 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 139 " - pdb=" SG  CYS L 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " 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
  Links applied
    ALPHA1-4
      " GLC A   1 " - " GLC A   2 "
  Time building additional restraints: 2.25
  Conformation dependent library (CDL) restraints added in 987.8 milliseconds
  

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2194

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 19 sheets defined
      36.9% alpha, 30.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.550A  pdb=" N   PHE H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'L' and resid 85 through 89
      removed outlier: 3.649A  pdb=" N   LEU L  89 " --> pdb=" O   PRO L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 126 through 132
    Processing helix  chain 'L' and resid 188 through 194
      removed outlier: 3.984A  pdb=" N   HIS L 194 " --> pdb=" O   ASP L 190 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'B' and resid 17 through 28
    Processing helix  chain 'B' and resid 43 through 52
      Proline residue:  B  49  - end of helix
    Processing helix  chain 'B' and resid 65 through 75
      removed outlier: 3.631A  pdb=" N   GLY B  69 " --> pdb=" O   HIS B  65 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   GLY B  70 " --> pdb=" O   ASP B  66 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   TYR B  71 " --> pdb=" O   ARG B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 89
    Processing helix  chain 'B' and resid 91 through 98
    Processing helix  chain 'B' and resid 129 through 131
      No H-bonds generated for 'chain 'B' and resid 129 through 131'
    Processing helix  chain 'B' and resid 132 through 141
    Processing helix  chain 'B' and resid 154 through 164
      removed outlier: 3.712A  pdb=" N   THR B 158 " --> pdb=" O   GLU B 154 " (cutoff:3.500A)
      Proline residue:  B 160  - end of helix
    Processing helix  chain 'B' and resid 186 through 202
    Processing helix  chain 'B' and resid 210 through 220
    Processing helix  chain 'B' and resid 231 through 240
      removed outlier: 4.545A  pdb=" N   ASN B 235 " --> pdb=" O   TRP B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 284
    Processing helix  chain 'B' and resid 287 through 298
      removed outlier: 3.868A  pdb=" N   ASP B 297 " --> pdb=" O   ALA B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 313
    Processing helix  chain 'B' and resid 315 through 328
    Processing helix  chain 'B' and resid 336 through 353
    Processing helix  chain 'B' and resid 357 through 370
    Processing helix  chain 'B' and resid 374 through 388
    Processing helix  chain 'B' and resid 391 through 406
    Processing helix  chain 'B' and resid 502 through 517
    Processing helix  chain 'K' and resid 3 through 27
    Processing helix  chain 'K' and resid 33 through 48
    Processing helix  chain 'K' and resid 49 through 52
      removed outlier: 4.196A  pdb=" N   PHE K  52 " --> pdb=" O   LEU K  49 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 49 through 52'
    Processing helix  chain 'K' and resid 57 through 80
    Processing helix  chain 'K' and resid 95 through 110
      Proline residue:  K 101  - end of helix
      removed outlier: 3.702A  pdb=" N   ASN K 110 " --> pdb=" O   SER K 106 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 114 through 129
    Processing helix  chain 'K' and resid 131 through 142
    Processing helix  chain 'K' and resid 148 through 173
    Processing helix  chain 'K' and resid 177 through 202
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.740A  pdb=" N   GLY H  33 " --> pdb=" O   ARG H  99 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ALA H  40 " --> pdb=" O   GLY H  44 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.344A  pdb=" N   TYR H 112 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 130 through 134
      removed outlier: 3.891A  pdb=" N   GLY H 149 " --> pdb=" O   LEU H 134 " (cutoff:3.500A)
      removed outlier: 5.307A  pdb=" N   GLY H 149 " --> pdb=" O   VAL H 192 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   VAL H 192 " --> pdb=" O   GLY H 149 " (cutoff:3.500A)
      removed outlier: 5.365A  pdb=" N   LEU H 151 " --> pdb=" O   SER H 190 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   SER H 190 " --> pdb=" O   LEU H 151 " (cutoff:3.500A)
      removed outlier: 4.971A  pdb=" N   LYS H 153 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   LEU H 188 " --> pdb=" O   LYS H 153 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 130 through 134
      removed outlier: 3.891A  pdb=" N   GLY H 149 " --> pdb=" O   LEU H 134 " (cutoff:3.500A)
      removed outlier: 5.307A  pdb=" N   GLY H 149 " --> pdb=" O   VAL H 192 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   VAL H 192 " --> pdb=" O   GLY H 149 " (cutoff:3.500A)
      removed outlier: 5.365A  pdb=" N   LEU H 151 " --> pdb=" O   SER H 190 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   SER H 190 " --> pdb=" O   LEU H 151 " (cutoff:3.500A)
      removed outlier: 4.971A  pdb=" N   LYS H 153 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   LEU H 188 " --> pdb=" O   LYS H 153 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   SER H 187 " --> pdb=" O   VAL H 179 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 161 through 164
      removed outlier: 6.586A  pdb=" N   LYS B 484 " --> pdb=" O   PHE B 532 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   VAL B 534 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   VAL B 486 " --> pdb=" O   VAL B 534 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 14
      removed outlier: 6.921A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 110 " (cutoff:3.500A)
      removed outlier: 7.398A  pdb=" N   LYS L 112 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   VAL L  13 " --> pdb=" O   LYS L 112 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA L  90 " --> pdb=" O   LEU L 109 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   LEU L  39 " --> pdb=" O   TYR L  55 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   TYR L  55 " --> pdb=" O   LEU L  39 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 14
      removed outlier: 6.921A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 110 " (cutoff:3.500A)
      removed outlier: 7.398A  pdb=" N   LYS L 112 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   VAL L  13 " --> pdb=" O   LYS L 112 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA L  90 " --> pdb=" O   LEU L 109 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 119 through 123
      removed outlier: 5.766A  pdb=" N   TYR L 178 " --> pdb=" O   ASN L 143 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 150 through 154
    Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 13
      removed outlier: 6.719A  pdb=" N   TRP N  32 " --> pdb=" O   ARG N  52 " (cutoff:3.500A)
      removed outlier: 4.940A  pdb=" N   ARG N  52 " --> pdb=" O   TRP N  32 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   MET N  34 " --> pdb=" O   ALA N  50 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   ALA N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'N' and resid 11 through 13
    Processing sheet with id=AB6, first strand: chain 'B' and resid 37 through 39
      removed outlier: 5.931A  pdb=" N   ILE B  10 " --> pdb=" O   GLU B  39 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   VAL B   9 " --> pdb=" O   ILE B  60 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   PHE B  62 " --> pdb=" O   VAL B   9 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   TRP B  11 " --> pdb=" O   PHE B  62 " (cutoff:3.500A)
      removed outlier: 8.666A  pdb=" N   ALA B  64 " --> pdb=" O   TRP B  11 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   GLY B 261 " --> pdb=" O   VAL B 111 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   VAL B 111 " --> pdb=" O   GLY B 261 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   LEU B 263 " --> pdb=" O   ILE B 109 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 37 through 39
      removed outlier: 5.931A  pdb=" N   ILE B  10 " --> pdb=" O   GLU B  39 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   VAL B   9 " --> pdb=" O   ILE B  60 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   PHE B  62 " --> pdb=" O   VAL B   9 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   TRP B  11 " --> pdb=" O   PHE B  62 " (cutoff:3.500A)
      removed outlier: 8.666A  pdb=" N   ALA B  64 " --> pdb=" O   TRP B  11 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 99 through 100
    Processing sheet with id=AB9, first strand: chain 'B' and resid 225 through 228
    Processing sheet with id=AC1, first strand: chain 'B' and resid 171 through 173
      removed outlier: 4.059A  pdb=" N   LYS B 171 " --> pdb=" O   ASP B 178 " (cutoff:3.500A)

    502 hydrogen bonds defined for protein.
    1368 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: 3.03

  Time building geometry restraints manager: 2.65 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1509
        1.31 -     1.44: 2699
        1.44 -     1.56: 5330
        1.56 -     1.69: 1
        1.69 -     1.81: 51
  Bond restraints: 9590
  Sorted by residual:
  bond pdb=" C29 POV K 304 "
       pdb="C210 POV K 304 "
    ideal  model  delta    sigma   weight residual
    1.333  1.528 -0.195 2.00e-02 2.50e+03 9.46e+01
  bond pdb=" C29 POV K 302 "
       pdb="C210 POV K 302 "
    ideal  model  delta    sigma   weight residual
    1.333  1.527 -0.194 2.00e-02 2.50e+03 9.42e+01
  bond pdb=" C29 POV K 303 "
       pdb="C210 POV K 303 "
    ideal  model  delta    sigma   weight residual
    1.333  1.527 -0.194 2.00e-02 2.50e+03 9.37e+01
  bond pdb=" C29 POV K 301 "
       pdb="C210 POV K 301 "
    ideal  model  delta    sigma   weight residual
    1.333  1.526 -0.193 2.00e-02 2.50e+03 9.27e+01
  bond pdb=" C21 POV K 302 "
       pdb=" O21 POV K 302 "
    ideal  model  delta    sigma   weight residual
    1.330  1.185  0.145 2.00e-02 2.50e+03 5.24e+01
  ... (remaining 9585 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.73: 12946
        3.73 -     7.46: 47
        7.46 -    11.19: 3
       11.19 -    14.92: 1
       14.92 -    18.65: 8
  Bond angle restraints: 13005
  Sorted by residual:
  angle pdb=" C29 POV K 301 "
        pdb="C210 POV K 301 "
        pdb="C211 POV K 301 "
      ideal   model   delta    sigma   weight residual
     127.67  109.02   18.65 3.00e+00 1.11e-01 3.86e+01
  angle pdb=" C28 POV K 303 "
        pdb=" C29 POV K 303 "
        pdb="C210 POV K 303 "
      ideal   model   delta    sigma   weight residual
     127.79  109.29   18.50 3.00e+00 1.11e-01 3.80e+01
  angle pdb=" C28 POV K 302 "
        pdb=" C29 POV K 302 "
        pdb="C210 POV K 302 "
      ideal   model   delta    sigma   weight residual
     127.79  109.32   18.47 3.00e+00 1.11e-01 3.79e+01
  angle pdb=" C29 POV K 303 "
        pdb="C210 POV K 303 "
        pdb="C211 POV K 303 "
      ideal   model   delta    sigma   weight residual
     127.67  109.31   18.36 3.00e+00 1.11e-01 3.75e+01
  angle pdb=" C28 POV K 301 "
        pdb=" C29 POV K 301 "
        pdb="C210 POV K 301 "
      ideal   model   delta    sigma   weight residual
     127.79  109.48   18.31 3.00e+00 1.11e-01 3.73e+01
  ... (remaining 13000 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 5128
       17.95 -    35.91: 428
       35.91 -    53.86: 92
       53.86 -    71.82: 17
       71.82 -    89.77: 10
  Dihedral angle restraints: 5675
    sinusoidal: 2250
      harmonic: 3425
  Sorted by residual:
  dihedral pdb=" CA  GLU H 158 "
           pdb=" C   GLU H 158 "
           pdb=" N   PRO H 159 "
           pdb=" CA  PRO H 159 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.16   31.84     0      5.00e+00 4.00e-02 4.05e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.49   45.51     1      1.00e+01 1.00e-02 2.87e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   58.52   34.48     1      1.00e+01 1.00e-02 1.69e+01
  ... (remaining 5672 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1243
       0.059 -    0.118: 181
       0.118 -    0.177: 14
       0.177 -    0.236: 1
       0.236 -    0.294: 1
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" C1  GLC A   2 "
            pdb=" O4  GLC A   1 "
            pdb=" C2  GLC A   2 "
            pdb=" O5  GLC A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.33    0.07 2.00e-02 2.50e+03 1.28e+01
  chirality pdb=" C1  GLC A   1 "
            pdb=" C2  GLC A   1 "
            pdb=" O1  GLC A   1 "
            pdb=" O5  GLC A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.04   -2.33    0.29 2.00e-01 2.50e+01 2.17e+00
  chirality pdb=" CA  ASN B 283 "
            pdb=" N   ASN B 283 "
            pdb=" C   ASN B 283 "
            pdb=" CB  ASN B 283 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.08e+00
  ... (remaining 1437 not shown)

  Planarity restraints: 1630
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV K 303 "   -0.278 2.00e-02 2.50e+03   2.79e-01 7.76e+02
        pdb=" C29 POV K 303 "    0.278 2.00e-02 2.50e+03
        pdb="C210 POV K 303 "    0.279 2.00e-02 2.50e+03
        pdb="C211 POV K 303 "   -0.279 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV K 304 "    0.172 2.00e-02 2.50e+03   1.72e-01 2.96e+02
        pdb=" C29 POV K 304 "   -0.173 2.00e-02 2.50e+03
        pdb="C210 POV K 304 "   -0.171 2.00e-02 2.50e+03
        pdb="C211 POV K 304 "    0.172 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV K 302 "   -0.147 2.00e-02 2.50e+03   1.47e-01 2.16e+02
        pdb=" C29 POV K 302 "    0.146 2.00e-02 2.50e+03
        pdb="C210 POV K 302 "    0.148 2.00e-02 2.50e+03
        pdb="C211 POV K 302 "   -0.147 2.00e-02 2.50e+03
  ... (remaining 1627 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 111
        2.65 -     3.21: 8507
        3.21 -     3.78: 14725
        3.78 -     4.34: 20837
        4.34 -     4.90: 34383
  Nonbonded interactions: 78563
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP K   9 "
            pdb=" OH  TYR K 162 "
     model   vdw
     2.089 3.040
  nonbonded pdb=" OH  TYR N 106 "
            pdb=" OD2 ASP K   9 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" OG1 THR K  45 "
            pdb=" OH  TYR K  72 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" O   ASN B 235 "
            pdb=" OG1 THR B 238 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" O   PRO H 129 "
            pdb=" OH  TYR B 513 "
     model   vdw
     2.182 3.040
  ... (remaining 78558 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     22.970
  Find NCS groups from input model:        0.120
  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:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.195   9590  Z= 0.328
  Angle     :  0.777  18.648  13005  Z= 0.348
  Chirality :  0.042   0.294   1440
  Planarity :  0.011   0.279   1630
  Dihedral  : 14.270  89.769   3466
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.92 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.24), residues: 1152
  helix:  1.83 (0.26), residues: 381
  sheet:  0.63 (0.28), residues: 305
  loop :  0.12 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP N 107 
 HIS   0.004   0.001   HIS L  95 
 PHE   0.030   0.001   PHE B 259 
 TYR   0.048   0.001   TYR K 162 
 ARG   0.005   0.000   ARG B  99 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.113 
Fit side-chains
REVERT: N   46 GLU cc_start: 0.7803 (pt0) cc_final: 0.7590 (pt0)
REVERT: K  201 LYS cc_start: 0.7742 (ttmt) cc_final: 0.7519 (ttpt)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2432
  time to fit residues: 47.8490
Evaluate side-chains
  118 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 46 optimal weight:    0.3980
   chunk 90 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0170
   chunk 67 optimal weight:    3.9990
   chunk 104 optimal weight:    5.9990
   overall best weight:    1.0420

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

Flipped N/Q/H residues before XYZ refinement:
H  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.172225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.130352 restraints weight = 12386.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 2.02
r_work: 0.3265 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3128 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.0990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9590  Z= 0.215
  Angle     :  0.537   7.496  13005  Z= 0.279
  Chirality :  0.040   0.149   1440
  Planarity :  0.005   0.123   1630
  Dihedral  :  7.172  69.181   1352
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  6.71 %
    Favored  : 92.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.92 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.25), residues: 1152
  helix:  1.95 (0.25), residues: 387
  sheet:  0.75 (0.29), residues: 305
  loop :  0.12 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 523 
 HIS   0.003   0.001   HIS L  95 
 PHE   0.019   0.001   PHE B 259 
 TYR   0.031   0.001   TYR K 162 
 ARG   0.003   0.000   ARG B  99 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 133
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
REVERT: H  153 LYS cc_start: 0.8359 (ttpt) cc_final: 0.7893 (ttmt)
REVERT: N   46 GLU cc_start: 0.8247 (pt0) cc_final: 0.8028 (pt0)
REVERT: B   39 GLU cc_start: 0.6931 (mp0) cc_final: 0.6416 (pm20)
REVERT: B  178 ASP cc_start: 0.7165 (t0) cc_final: 0.6117 (p0)
REVERT: B  323 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8104 (tt0)
REVERT: K  201 LYS cc_start: 0.7988 (ttmt) cc_final: 0.7592 (ttpt)
  outliers start: 6
  outliers final: 4
  residues processed: 135
  average time/residue: 0.2298
  time to fit residues: 42.5657
Evaluate side-chains
  126 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 122
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  131 VAL
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue  181 SER
Chi-restraints excluded: chain K residue   53 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9990
   chunk 18 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0170
   chunk 88 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 85 optimal weight:    3.9990
   overall best weight:    0.9622

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

Flipped N/Q/H residues before XYZ refinement:
B 356 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.173481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.130911 restraints weight = 12597.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 2.11
r_work: 0.3260 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.1235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9590  Z= 0.193
  Angle     :  0.506   5.975  13005  Z= 0.262
  Chirality :  0.040   0.165   1440
  Planarity :  0.004   0.102   1630
  Dihedral  :  6.695  54.406   1352
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  8.71 %
    Favored  : 90.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.92 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.25), residues: 1152
  helix:  2.17 (0.26), residues: 386
  sheet:  0.77 (0.28), residues: 312
  loop :  0.17 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 159 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.015   0.001   PHE B 259 
 TYR   0.019   0.001   TYR K 162 
 ARG   0.002   0.000   ARG H  19 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 133
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
REVERT: H  153 LYS cc_start: 0.8329 (ttpt) cc_final: 0.8078 (ttpt)
REVERT: L  175 ASP cc_start: 0.7924 (t0) cc_final: 0.7717 (t0)
REVERT: N   46 GLU cc_start: 0.8312 (pt0) cc_final: 0.8081 (pt0)
REVERT: B   23 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6591 (mp0)
REVERT: B  178 ASP cc_start: 0.7066 (t0) cc_final: 0.6044 (p0)
REVERT: B  323 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8134 (tt0)
REVERT: K   33 SER cc_start: 0.8909 (t) cc_final: 0.8577 (m)
REVERT: K  134 GLN cc_start: 0.8702 (tp40) cc_final: 0.8253 (tp-100)
  outliers start: 12
  outliers final: 6
  residues processed: 139
  average time/residue: 0.2334
  time to fit residues: 44.4596
Evaluate side-chains
  134 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 127
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  131 VAL
Chi-restraints excluded: chain H residue  192 VAL
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue  181 SER
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue  487 ILE
Chi-restraints excluded: chain K residue   53 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 56 optimal weight:    7.9990
   chunk 108 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 91 optimal weight:   20.0000
   chunk 83 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 112 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 80 optimal weight:    9.9990
   chunk 29 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 356 GLN
B 366 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.158549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.103583 restraints weight = 12259.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 1.97
r_work: 0.3038 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.110   9590  Z= 0.613
  Angle     :  0.714   7.265  13005  Z= 0.367
  Chirality :  0.047   0.195   1440
  Planarity :  0.005   0.088   1630
  Dihedral  :  7.781  58.591   1352
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 11.81 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  0.88 (0.24), residues: 1152
  helix:  1.55 (0.25), residues: 388
  sheet:  0.46 (0.28), residues: 311
  loop : -0.07 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP N  32 
 HIS   0.006   0.001   HIS H  35 
 PHE   0.024   0.002   PHE B 259 
 TYR   0.025   0.002   TYR K 158 
 ARG   0.004   0.001   ARG H  72 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
REVERT: H   89 GLU cc_start: 0.8062 (mp0) cc_final: 0.7677 (pt0)
REVERT: H  153 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7952 (ttpt)
REVERT: L  175 ASP cc_start: 0.7618 (t0) cc_final: 0.7209 (t0)
REVERT: L  193 LYS cc_start: 0.6810 (pptt) cc_final: 0.6467 (pttt)
REVERT: B   23 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.6510 (mp0)
REVERT: B  178 ASP cc_start: 0.7279 (t0) cc_final: 0.6168 (p0)
REVERT: B  323 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7945 (tt0)
REVERT: B  366 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8194 (mm-40)
REVERT: K   33 SER cc_start: 0.8924 (t) cc_final: 0.8517 (m)
REVERT: K   42 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8529 (tp)
REVERT: K  134 GLN cc_start: 0.8783 (tp40) cc_final: 0.8029 (tp-100)
  outliers start: 18
  outliers final: 13
  residues processed: 141
  average time/residue: 0.2493
  time to fit residues: 48.2209
Evaluate side-chains
  139 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  131 VAL
Chi-restraints excluded: chain H residue  192 VAL
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue  181 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  356 GLN
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  524 THR
Chi-restraints excluded: chain K residue   42 LEU
Chi-restraints excluded: chain K residue   53 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 79 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 89 optimal weight:    0.6980
   chunk 84 optimal weight:    4.9990
   chunk 113 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 366 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.162965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.108432 restraints weight = 12159.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 2.17
r_work: 0.3083 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   9590  Z= 0.232
  Angle     :  0.540   7.586  13005  Z= 0.280
  Chirality :  0.041   0.204   1440
  Planarity :  0.004   0.058   1630
  Dihedral  :  7.080  57.781   1352
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.81 %
    Favored  : 85.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.25), residues: 1152
  helix:  1.93 (0.25), residues: 385
  sheet:  0.50 (0.28), residues: 315
  loop :  0.06 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.006   0.001   HIS L 194 
 PHE   0.025   0.001   PHE L 144 
 TYR   0.013   0.001   TYR H  95 
 ARG   0.005   0.000   ARG B 355 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
REVERT: H  153 LYS cc_start: 0.8057 (ttpt) cc_final: 0.7813 (ttpt)
REVERT: L  193 LYS cc_start: 0.7037 (pptt) cc_final: 0.6687 (pttt)
REVERT: B   23 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6425 (mp0)
REVERT: B  178 ASP cc_start: 0.7127 (t0) cc_final: 0.5939 (p0)
REVERT: B  323 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7881 (tt0)
REVERT: K   33 SER cc_start: 0.8963 (t) cc_final: 0.8213 (m)
REVERT: K  134 GLN cc_start: 0.8715 (tp40) cc_final: 0.8123 (tp-100)
  outliers start: 16
  outliers final: 10
  residues processed: 145
  average time/residue: 0.2256
  time to fit residues: 45.2379
Evaluate side-chains
  140 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain H residue  131 VAL
Chi-restraints excluded: chain H residue  192 VAL
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue  181 SER
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain K residue   53 THR
Chi-restraints excluded: chain K residue  138 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   chunk 78 optimal weight:    8.9990
   chunk 76 optimal weight:    0.2980
   chunk 9 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 95 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 99 optimal weight:    0.4980
   chunk 57 optimal weight:    4.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 356 GLN
B 366 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.163812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.109543 restraints weight = 12135.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 2.11
r_work: 0.3124 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9590  Z= 0.192
  Angle     :  0.516   8.893  13005  Z= 0.265
  Chirality :  0.040   0.206   1440
  Planarity :  0.004   0.052   1630
  Dihedral  :  6.482  59.345   1352
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 13.01 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.25), residues: 1152
  helix:  2.20 (0.26), residues: 385
  sheet:  0.57 (0.28), residues: 322
  loop :  0.06 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.004   0.001   HIS L 194 
 PHE   0.022   0.001   PHE L 144 
 TYR   0.011   0.001   TYR H  95 
 ARG   0.003   0.000   ARG B  99 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
REVERT: H  153 LYS cc_start: 0.8046 (ttpt) cc_final: 0.7838 (ttpt)
REVERT: L  193 LYS cc_start: 0.6963 (pptt) cc_final: 0.6655 (pttt)
REVERT: B   23 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6436 (mp0)
REVERT: B   39 GLU cc_start: 0.7006 (mp0) cc_final: 0.6390 (pm20)
REVERT: B  178 ASP cc_start: 0.7016 (t0) cc_final: 0.5771 (p0)
REVERT: B  283 ASN cc_start: 0.8114 (m-40) cc_final: 0.7910 (m110)
REVERT: B  323 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7884 (tt0)
REVERT: K   33 SER cc_start: 0.8924 (t) cc_final: 0.8409 (m)
REVERT: K  134 GLN cc_start: 0.8699 (tp40) cc_final: 0.8032 (tp-100)
  outliers start: 19
  outliers final: 12
  residues processed: 148
  average time/residue: 0.2309
  time to fit residues: 47.3384
Evaluate side-chains
  142 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain H residue  131 VAL
Chi-restraints excluded: chain H residue  192 VAL
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue  181 SER
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  185 ASP
Chi-restraints excluded: chain K residue   53 THR
Chi-restraints excluded: chain K residue  138 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 104 optimal weight:    0.3980
   chunk 8 optimal weight:    5.9990
   chunk 114 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 92 optimal weight:   20.0000
   chunk 98 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 89 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 82 optimal weight:    0.8980
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
L 194 HIS
B 366 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.163175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.108518 restraints weight = 12310.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.10
r_work: 0.3106 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9590  Z= 0.239
  Angle     :  0.533   8.947  13005  Z= 0.272
  Chirality :  0.040   0.213   1440
  Planarity :  0.004   0.042   1630
  Dihedral  :  6.350  59.857   1352
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 13.91 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.25), residues: 1152
  helix:  2.22 (0.26), residues: 385
  sheet:  0.57 (0.28), residues: 322
  loop :  0.06 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  47 
 HIS   0.004   0.001   HIS L  95 
 PHE   0.021   0.001   PHE K  97 
 TYR   0.012   0.001   TYR H  95 
 ARG   0.003   0.000   ARG B  99 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
REVERT: L  192 GLU cc_start: 0.6396 (mm-30) cc_final: 0.5672 (tm-30)
REVERT: L  193 LYS cc_start: 0.7003 (pptt) cc_final: 0.6440 (pttt)
REVERT: B   23 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6430 (mp0)
REVERT: B   39 GLU cc_start: 0.7028 (mp0) cc_final: 0.6345 (pm20)
REVERT: B  178 ASP cc_start: 0.7012 (t0) cc_final: 0.5764 (p0)
REVERT: B  323 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7891 (tt0)
REVERT: K   33 SER cc_start: 0.8950 (t) cc_final: 0.8417 (m)
REVERT: K  134 GLN cc_start: 0.8706 (tp40) cc_final: 0.8022 (tp-100)
  outliers start: 18
  outliers final: 16
  residues processed: 141
  average time/residue: 0.2240
  time to fit residues: 43.9615
Evaluate side-chains
  144 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   43 MET
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain H residue  131 VAL
Chi-restraints excluded: chain H residue  192 VAL
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue  181 SER
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  185 ASP
Chi-restraints excluded: chain K residue   42 LEU
Chi-restraints excluded: chain K residue   53 THR
Chi-restraints excluded: chain K residue  138 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 88 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 114 optimal weight:    4.9990
   chunk 95 optimal weight:    0.0670
   chunk 94 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 87 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
B 366 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.165160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.110964 restraints weight = 12301.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.18
r_work: 0.3136 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   9590  Z= 0.161
  Angle     :  0.515   9.647  13005  Z= 0.263
  Chirality :  0.040   0.200   1440
  Planarity :  0.003   0.042   1630
  Dihedral  :  5.930  59.615   1352
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.31 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.25), residues: 1152
  helix:  2.38 (0.26), residues: 385
  sheet:  0.66 (0.28), residues: 323
  loop :  0.07 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.004   0.001   HIS L 194 
 PHE   0.020   0.001   PHE K  97 
 TYR   0.012   0.001   TYR B 525 
 ARG   0.003   0.000   ARG B  99 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
REVERT: L  192 GLU cc_start: 0.6395 (mm-30) cc_final: 0.5695 (pp20)
REVERT: L  193 LYS cc_start: 0.7191 (pptt) cc_final: 0.6326 (pptt)
REVERT: B   23 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6476 (mp0)
REVERT: B   39 GLU cc_start: 0.7035 (mp0) cc_final: 0.6362 (pm20)
REVERT: B  178 ASP cc_start: 0.6967 (t0) cc_final: 0.5714 (p0)
REVERT: B  323 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7843 (tt0)
REVERT: K   33 SER cc_start: 0.8941 (t) cc_final: 0.8383 (m)
REVERT: K  134 GLN cc_start: 0.8722 (tp40) cc_final: 0.8092 (tp-100)
  outliers start: 18
  outliers final: 13
  residues processed: 148
  average time/residue: 0.2123
  time to fit residues: 44.2370
Evaluate side-chains
  145 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   43 MET
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain H residue  131 VAL
Chi-restraints excluded: chain H residue  192 VAL
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue  181 SER
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  185 ASP
Chi-restraints excluded: chain K residue   53 THR
Chi-restraints excluded: chain K residue  138 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 101 optimal weight:    5.9990
   chunk 78 optimal weight:    6.9990
   chunk 95 optimal weight:    0.7980
   chunk 81 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   chunk 91 optimal weight:    9.9990
   chunk 97 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 98 optimal weight:    0.8980
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
B 283 ASN
B 366 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.162682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.108226 restraints weight = 12256.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.07
r_work: 0.3100 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   9590  Z= 0.275
  Angle     :  0.560  10.245  13005  Z= 0.285
  Chirality :  0.041   0.213   1440
  Planarity :  0.004   0.041   1630
  Dihedral  :  6.110  56.488   1352
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.61 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.25), residues: 1152
  helix:  2.30 (0.26), residues: 385
  sheet:  0.58 (0.28), residues: 324
  loop :  0.04 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP N  32 
 HIS   0.005   0.001   HIS L  95 
 PHE   0.026   0.002   PHE K  97 
 TYR   0.013   0.001   TYR H  95 
 ARG   0.003   0.000   ARG B  99 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
REVERT: L  192 GLU cc_start: 0.6383 (mm-30) cc_final: 0.5704 (pp20)
REVERT: L  193 LYS cc_start: 0.7183 (pptt) cc_final: 0.6299 (pptt)
REVERT: B   23 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6444 (mp0)
REVERT: B   39 GLU cc_start: 0.7043 (mp0) cc_final: 0.6375 (pm20)
REVERT: B  178 ASP cc_start: 0.6928 (t0) cc_final: 0.5723 (p0)
REVERT: B  284 TYR cc_start: 0.7266 (m-80) cc_final: 0.6992 (m-80)
REVERT: B  323 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7848 (tt0)
REVERT: B  366 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7891 (mm-40)
REVERT: K   33 SER cc_start: 0.8959 (t) cc_final: 0.8420 (m)
REVERT: K  134 GLN cc_start: 0.8708 (tp40) cc_final: 0.7992 (tp-100)
  outliers start: 20
  outliers final: 16
  residues processed: 141
  average time/residue: 0.2395
  time to fit residues: 47.4179
Evaluate side-chains
  143 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   43 MET
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain H residue  131 VAL
Chi-restraints excluded: chain H residue  192 VAL
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue  181 SER
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  107 TYR
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  185 ASP
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain K residue   53 THR
Chi-restraints excluded: chain K residue  138 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 112 optimal weight:    0.7980
   chunk 109 optimal weight:    6.9990
   chunk 66 optimal weight:    7.9990
   chunk 43 optimal weight:    3.9990
   chunk 91 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0070
   chunk 46 optimal weight:    0.2980
   chunk 86 optimal weight:    0.8980
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
B 366 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.164866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.110324 restraints weight = 12261.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 2.16
r_work: 0.3135 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9590  Z= 0.167
  Angle     :  0.531  10.828  13005  Z= 0.269
  Chirality :  0.040   0.195   1440
  Planarity :  0.003   0.042   1630
  Dihedral  :  5.825  55.288   1352
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 14.91 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.25), residues: 1152
  helix:  2.41 (0.26), residues: 385
  sheet:  0.67 (0.28), residues: 323
  loop :  0.04 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.003   0.001   HIS L 194 
 PHE   0.029   0.001   PHE K  97 
 TYR   0.020   0.001   TYR K  76 
 ARG   0.003   0.000   ARG B  99 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
REVERT: H  214 ASN cc_start: 0.8363 (t0) cc_final: 0.7545 (m-40)
REVERT: L  192 GLU cc_start: 0.6299 (mm-30) cc_final: 0.5611 (pp20)
REVERT: L  193 LYS cc_start: 0.7028 (pptt) cc_final: 0.6170 (pptt)
REVERT: B   23 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6466 (mp0)
REVERT: B   39 GLU cc_start: 0.7039 (mp0) cc_final: 0.6357 (pm20)
REVERT: B  178 ASP cc_start: 0.6871 (t0) cc_final: 0.5656 (p0)
REVERT: B  284 TYR cc_start: 0.7213 (m-80) cc_final: 0.6922 (m-80)
REVERT: B  312 LEU cc_start: 0.6960 (tp) cc_final: 0.6515 (pp)
REVERT: B  323 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7844 (tt0)
REVERT: K   33 SER cc_start: 0.8934 (t) cc_final: 0.8381 (m)
REVERT: K  127 GLU cc_start: 0.8596 (tt0) cc_final: 0.8359 (tt0)
REVERT: K  134 GLN cc_start: 0.8719 (tp40) cc_final: 0.8074 (tp-100)
  outliers start: 17
  outliers final: 15
  residues processed: 139
  average time/residue: 0.2163
  time to fit residues: 42.1197
Evaluate side-chains
  142 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   43 MET
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain H residue  131 VAL
Chi-restraints excluded: chain H residue  192 VAL
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue  181 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  185 ASP
Chi-restraints excluded: chain K residue   53 THR
Chi-restraints excluded: chain K residue  138 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 94 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   chunk 23 optimal weight:    0.5980
   chunk 78 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 90 optimal weight:    6.9990
   chunk 68 optimal weight:    9.9990
   chunk 89 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
B 366 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.161948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.108439 restraints weight = 12178.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.04
r_work: 0.3099 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   9590  Z= 0.297
  Angle     :  0.578  10.617  13005  Z= 0.293
  Chirality :  0.041   0.194   1440
  Planarity :  0.004   0.043   1630
  Dihedral  :  6.101  52.599   1352
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.02 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.25), residues: 1152
  helix:  2.30 (0.26), residues: 385
  sheet:  0.54 (0.28), residues: 324
  loop :  0.03 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP N  32 
 HIS   0.006   0.001   HIS L  95 
 PHE   0.029   0.002   PHE K  97 
 TYR   0.014   0.001   TYR L  38 
 ARG   0.006   0.000   ARG B  99 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6430.63 seconds
wall clock time: 111 minutes 31.31 seconds (6691.31 seconds total)