Starting phenix.real_space_refine
on Wed Mar 12 05:50:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y52_38928/03_2025/8y52_38928.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y52_38928/03_2025/8y52_38928.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y52_38928/03_2025/8y52_38928.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y52_38928/03_2025/8y52_38928.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y52_38928/03_2025/8y52_38928.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y52_38928/03_2025/8y52_38928.cif"
  }
  resolution = 2.9
  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=   0.057
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      45      5.16       5
     C    4706      2.51       5
     N    1272      2.21       5
     O    1357      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 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: 7380
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1908
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1908
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2592
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "G"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 407
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 3, 'TRANS': 50}
    Chain: "R"
      Number of atoms: 2392
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2392
          Classifications: {'peptide': 299}
          Link IDs: {'PTRANS': 12, 'TRANS': 286}
    Chain: "X"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 81
          Unusual residues: {'BAL': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Modifications used: {'PEPT-D': 1}
          Link IDs: {'POST-BETA-TRANS': 1, 'PRE-BETA-TRANS': 1, 'TRANS': 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'BAL:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 4.93, per 1000 atoms: 0.67
  Number of scatterers: 7380
  At special positions: 0
  Unit cell: (88.4, 82.16, 134.16, 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      45     16.00
     O    1357      8.00
     N    1272      7.00
     C    4706      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 120 " - pdb=" SG  CYS R 203 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.04
  Conformation dependent library (CDL) restraints added in 998.8 milliseconds
  

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DPN X   1 "
  Number of C-beta restraints generated:  1776

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 9 sheets defined
      46.9% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 210 through 216
      removed outlier: 3.606A  pdb=" N   CYS A 214 " --> pdb=" O   TRP A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 245
    Processing helix  chain 'A' and resid 260 through 271
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 279 through 283
    Processing helix  chain 'A' and resid 298 through 318
      removed outlier: 3.591A  pdb=" N   PHE A 312 " --> pdb=" O   ILE A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 358
    Processing helix  chain 'B' and resid 9 through 30
      removed outlier: 3.556A  pdb=" N   CYS B  30 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 39
      removed outlier: 3.531A  pdb=" N   ILE B  38 " --> pdb=" O   THR B  34 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 28 through 44
      removed outlier: 3.523A  pdb=" N   ALA G  32 " --> pdb=" O   LYS G  28 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 47
      No H-bonds generated for 'chain 'G' and resid 45 through 47'
    Processing helix  chain 'R' and resid 50 through 75
    Processing helix  chain 'R' and resid 76 through 79
    Processing helix  chain 'R' and resid 82 through 108
      removed outlier: 3.608A  pdb=" N   ILE R  86 " --> pdb=" O   PRO R  82 " (cutoff:3.500A)
      Proline residue:  R 102  - end of helix
    Processing helix  chain 'R' and resid 115 through 150
    Processing helix  chain 'R' and resid 151 through 155
      removed outlier: 3.629A  pdb=" N   ARG R 155 " --> pdb=" O   PRO R 152 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 160 through 186
      removed outlier: 3.668A  pdb=" N   THR R 164 " --> pdb=" O   ALA R 160 " (cutoff:3.500A)
      Proline residue:  R 181  - end of helix
    Processing helix  chain 'R' and resid 207 through 209
      No H-bonds generated for 'chain 'R' and resid 207 through 209'
    Processing helix  chain 'R' and resid 210 through 226
    Processing helix  chain 'R' and resid 226 through 251
    Processing helix  chain 'R' and resid 259 through 298
      removed outlier: 3.634A  pdb=" N   VAL R 277 " --> pdb=" O   VAL R 273 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ALA R 278 " --> pdb=" O   LEU R 274 " (cutoff:3.500A)
      Proline residue:  R 286  - end of helix
    Processing helix  chain 'R' and resid 307 through 334
      removed outlier: 4.045A  pdb=" N   PHE R 311 " --> pdb=" O   MET R 307 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ASN R 322 " --> pdb=" O   LEU R 318 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   SER R 323 " --> pdb=" O   ALA R 319 " (cutoff:3.500A)
      Proline residue:  R 327  - end of helix
      removed outlier: 3.506A  pdb=" N   SER R 334 " --> pdb=" O   LEU R 330 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 335 through 345
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.518A  pdb=" N   LEU A  34 " --> pdb=" O   HIS A 197 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 9.930A  pdb=" N   ALA A 220 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.337A  pdb=" N   ILE A 222 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56
      removed outlier: 5.243A  pdb=" N   THR B  52 " --> pdb=" O   ASN B 345 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   ASN B 345 " --> pdb=" O   THR B  52 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU B 341 " --> pdb=" O   LEU B  56 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68
      removed outlier: 3.514A  pdb=" N   ALA B  65 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LYS B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   LEU B  84 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ALA B  97 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ILE B  86 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110
      removed outlier: 6.682A  pdb=" N   GLY B 120 " --> pdb=" O   MET B 106 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   CYS B 108 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA B 118 " --> pdb=" O   CYS B 108 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   TYR B 110 " --> pdb=" O   TYR B 116 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   TYR B 116 " --> pdb=" O   TYR B 110 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   CYS B 119 " --> pdb=" O   SER B 127 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   SER B 127 " --> pdb=" O   CYS B 119 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   GLY B 121 " --> pdb=" O   ILE B 125 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   ILE B 125 " --> pdb=" O   GLY B 121 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ASN B 130 " --> pdb=" O   VAL B 140 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   VAL B 140 " --> pdb=" O   ASN B 130 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156
      removed outlier: 3.665A  pdb=" N   CYS B 153 " --> pdb=" O   SER B 165 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   SER B 166 " --> pdb=" O   THR B 170 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   THR B 170 " --> pdb=" O   SER B 166 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ASP B 175 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   GLN B 181 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197
      removed outlier: 7.104A  pdb=" N   GLY B 207 " --> pdb=" O   MET B 193 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   LEU B 195 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   VAL B 205 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   LEU B 197 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   LEU B 203 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ALA B 213 " --> pdb=" O   THR B 226 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   THR B 226 " --> pdb=" O   ALA B 213 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   LEU B 215 " --> pdb=" O   ARG B 224 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239
      removed outlier: 6.168A  pdb=" N   CYS B 255 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   THR B 268 " --> pdb=" O   CYS B 255 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   LEU B 257 " --> pdb=" O   LEU B 266 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLN B 264 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283
      removed outlier: 3.755A  pdb=" N   SER B 280 " --> pdb=" O   GLY B 293 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ASN B 298 " --> pdb=" O   TYR B 294 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   ASP B 303 " --> pdb=" O   ARG B 309 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   ARG B 309 " --> pdb=" O   ASP B 303 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 187 through 193
      removed outlier: 3.570A  pdb=" N   MET R 198 " --> pdb=" O   ASP R 193 " (cutoff:3.500A)

    399 hydrogen bonds defined for protein.
    1158 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: 2.03

  Time building geometry restraints manager: 2.32 seconds

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

  Histogram of bond lengths:
        1.15 -     1.29: 1194
        1.29 -     1.42: 1976
        1.42 -     1.55: 4296
        1.55 -     1.68: 2
        1.68 -     1.81: 62
  Bond restraints: 7530
  Sorted by residual:
  bond pdb=" C   BAL X   6 "
       pdb=" N   HIS X   7 "
    ideal  model  delta    sigma   weight residual
    1.343  1.500 -0.157 1.40e-02 5.10e+03 1.26e+02
  bond pdb=" C   VAL X   5 "
       pdb=" N   BAL X   6 "
    ideal  model  delta    sigma   weight residual
    1.334  1.268  0.066 1.40e-02 5.10e+03 2.20e+01
  bond pdb=" CA  BAL X   6 "
       pdb=" CB  BAL X   6 "
    ideal  model  delta    sigma   weight residual
    1.521  1.371  0.150 3.30e-02 9.18e+02 2.06e+01
  bond pdb=" C   VAL X   5 "
       pdb=" O   VAL X   5 "
    ideal  model  delta    sigma   weight residual
    1.231  1.154  0.077 2.00e-02 2.50e+03 1.48e+01
  bond pdb=" N   BAL X   6 "
       pdb=" CB  BAL X   6 "
    ideal  model  delta    sigma   weight residual
    1.458  1.416  0.042 2.00e-02 2.50e+03 4.39e+00
  ... (remaining 7525 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.85: 10192
        5.85 -    11.70: 3
       11.70 -    17.55: 1
       17.55 -    23.40: 2
       23.40 -    29.25: 1
  Bond angle restraints: 10199
  Sorted by residual:
  angle pdb=" C   BAL X   6 "
        pdb=" CA  BAL X   6 "
        pdb=" CB  BAL X   6 "
      ideal   model   delta    sigma   weight residual
     110.50  139.75  -29.25 1.50e+00 4.44e-01 3.80e+02
  angle pdb=" CA  BAL X   6 "
        pdb=" C   BAL X   6 "
        pdb=" N   HIS X   7 "
      ideal   model   delta    sigma   weight residual
     115.94   93.57   22.36 2.00e+00 2.50e-01 1.25e+02
  angle pdb=" C   BAL X   6 "
        pdb=" N   HIS X   7 "
        pdb=" CA  HIS X   7 "
      ideal   model   delta    sigma   weight residual
     120.82  102.16   18.66 1.80e+00 3.09e-01 1.07e+02
  angle pdb=" CA  BAL X   6 "
        pdb=" C   BAL X   6 "
        pdb=" O   BAL X   6 "
      ideal   model   delta    sigma   weight residual
     120.80  135.52  -14.72 1.70e+00 3.46e-01 7.49e+01
  angle pdb=" O   BAL X   6 "
        pdb=" C   BAL X   6 "
        pdb=" N   HIS X   7 "
      ideal   model   delta    sigma   weight residual
     121.31  130.05   -8.74 1.60e+00 3.91e-01 2.98e+01
  ... (remaining 10194 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.63: 4416
       18.63 -    37.26: 75
       37.26 -    55.90: 11
       55.90 -    74.53: 4
       74.53 -    93.16: 3
  Dihedral angle restraints: 4509
    sinusoidal: 1777
      harmonic: 2732
  Sorted by residual:
  dihedral pdb=" N   BAL X   6 "
           pdb=" C   BAL X   6 "
           pdb=" CA  BAL X   6 "
           pdb=" CB  BAL X   6 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80   29.64   93.16     0      2.50e+00 1.60e-01 1.39e+03
  dihedral pdb=" C   BAL X   6 "
           pdb=" N   BAL X   6 "
           pdb=" CA  BAL X   6 "
           pdb=" CB  BAL X   6 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -33.78  -88.82     0      2.50e+00 1.60e-01 1.26e+03
  dihedral pdb=" CB  CYS R 120 "
           pdb=" SG  CYS R 120 "
           pdb=" SG  CYS R 203 "
           pdb=" CB  CYS R 203 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  144.41  -51.41     1      1.00e+01 1.00e-02 3.61e+01
  ... (remaining 4506 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1033
       0.060 -    0.120: 127
       0.120 -    0.179: 8
       0.179 -    0.239: 0
       0.239 -    0.299: 1
  Chirality restraints: 1169
  Sorted by residual:
  chirality pdb=" CA  HIS X   7 "
            pdb=" N   HIS X   7 "
            pdb=" C   HIS X   7 "
            pdb=" CB  HIS X   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" CA  ILE B  98 "
            pdb=" N   ILE B  98 "
            pdb=" C   ILE B  98 "
            pdb=" CB  ILE B  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.98e-01
  chirality pdb=" CA  ILE R 251 "
            pdb=" N   ILE R 251 "
            pdb=" C   ILE R 251 "
            pdb=" CB  ILE R 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.41e-01
  ... (remaining 1166 not shown)

  Planarity restraints: 1288
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  BAL X   6 "   -0.014 2.00e-02 2.50e+03   3.00e-02 8.99e+00
        pdb=" C   BAL X   6 "    0.051 2.00e-02 2.50e+03
        pdb=" O   BAL X   6 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   HIS X   7 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL X   5 "   -0.014 2.00e-02 2.50e+03   2.84e-02 8.09e+00
        pdb=" C   VAL X   5 "    0.049 2.00e-02 2.50e+03
        pdb=" O   VAL X   5 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   BAL X   6 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP X   3 "    0.022 2.00e-02 2.50e+03   1.09e-02 2.96e+00
        pdb=" CG  TRP X   3 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP X   3 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP X   3 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP X   3 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP X   3 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP X   3 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP X   3 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP X   3 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP X   3 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1285 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.62: 103
        2.62 -     3.19: 7105
        3.19 -     3.76: 11405
        3.76 -     4.33: 15922
        4.33 -     4.90: 26608
  Nonbonded interactions: 61143
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 286 "
            pdb=" OD2 ASP G  47 "
     model   vdw
     2.056 3.040
  nonbonded pdb=" O   ILE B 128 "
            pdb=" OG  SER B 141 "
     model   vdw
     2.096 3.040
  nonbonded pdb=" OD2 ASP B 210 "
            pdb=" OG  SER B 212 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" OD1 ASN A 216 "
            pdb=" NZ  LYS B  62 "
     model   vdw
     2.155 3.120
  nonbonded pdb=" OG  SER B  79 "
            pdb=" OD1 ASP B  81 "
     model   vdw
     2.164 3.040
  ... (remaining 61138 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:             1.280
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.920
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:89.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  112.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.157   7530  Z= 0.311
  Angle     :  0.622  29.248  10199  Z= 0.363
  Chirality :  0.038   0.299   1169
  Planarity :  0.003   0.031   1288
  Dihedral  :  7.692  82.149   2730
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  2.60 %
    Favored  : 97.15 %
  Cbeta Deviations :  0.22 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.26), residues: 915
  helix:  0.11 (0.25), residues: 405
  sheet: -1.93 (0.33), residues: 200
  loop : -1.63 (0.32), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP X   3 
 HIS   0.005   0.001   HIS R 340 
 PHE   0.006   0.001   PHE A 189 
 TYR   0.004   0.000   TYR R 237 
 ARG   0.002   0.000   ARG A 323 

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 219
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   47 ASP cc_start: 0.5409 (t0) cc_final: 0.4845 (t0)
REVERT: G   49 LEU cc_start: 0.6152 (mp) cc_final: 0.5659 (mp)
REVERT: R  104 ASP cc_start: 0.5609 (m-30) cc_final: 0.5154 (m-30)
REVERT: R  258 HIS cc_start: 0.4225 (t70) cc_final: 0.3915 (t70)
  outliers start: 2
  outliers final: 1
  residues processed: 220
  average time/residue: 1.2938
  time to fit residues: 299.8065
Evaluate side-chains
  105 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   86 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   chunk 46 optimal weight:    1.9990
   chunk 36 optimal weight:    8.9990
   chunk 70 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** A  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 300 ASN
R 258 HIS
R 322 ASN
X   2 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.071290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.056542 restraints weight = 29112.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 4.02
r_work: 0.3077 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.375   7530  Z= 0.678
  Angle     :  0.963  22.548  10199  Z= 0.502
  Chirality :  0.050   0.445   1169
  Planarity :  0.006   0.077   1288
  Dihedral  :  3.803  51.614   1020
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 21.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 16.98 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.27), residues: 915
  helix:  0.47 (0.25), residues: 407
  sheet: -1.70 (0.33), residues: 202
  loop : -1.46 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  87 
 HIS   0.009   0.001   HIS R 308 
 PHE   0.021   0.002   PHE A 343 
 TYR   0.011   0.002   TYR R  54 
 ARG   0.015   0.001   ARG G  26 

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.9232 (m-30) cc_final: 0.8956 (m-30)
REVERT: A   51 LYS cc_start: 0.9622 (mttp) cc_final: 0.9398 (tmmt)
REVERT: A  186 GLU cc_start: 0.8923 (tt0) cc_final: 0.8503 (tp30)
REVERT: A  198 MET cc_start: 0.9391 (ttm) cc_final: 0.9067 (ttp)
REVERT: B  219 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.6548 (mpp80)
REVERT: B  222 MET cc_start: 0.7979 (ppp) cc_final: 0.6066 (ppp)
REVERT: B  280 SER cc_start: 0.9338 (OUTLIER) cc_final: 0.9029 (p)
REVERT: B  306 LYS cc_start: 0.8842 (mmtp) cc_final: 0.8634 (mmtm)
REVERT: G   28 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.9081 (mmmt)
REVERT: G   31 LYS cc_start: 0.9034 (tptp) cc_final: 0.8707 (tptp)
REVERT: R  104 ASP cc_start: 0.7392 (m-30) cc_final: 0.6688 (m-30)
REVERT: R  136 PHE cc_start: 0.7527 (m-10) cc_final: 0.7029 (m-10)
REVERT: R  170 CYS cc_start: 0.8470 (p) cc_final: 0.8220 (p)
REVERT: R  224 VAL cc_start: 0.9608 (t) cc_final: 0.9372 (p)
REVERT: R  237 TYR cc_start: 0.7600 (m-10) cc_final: 0.7365 (m-10)
  outliers start: 27
  outliers final: 10
  residues processed: 125
  average time/residue: 1.2004
  time to fit residues: 158.8262
Evaluate side-chains
  110 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  274 LYS
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain G residue   12 ARG
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain R residue  129 THR
Chi-restraints excluded: chain R residue  133 VAL
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  308 HIS
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 58 optimal weight:    9.9990
   chunk 89 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 22 optimal weight:    0.2980
   chunk 4 optimal weight:    0.9980
   chunk 73 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0670
   chunk 33 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
** A  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.071767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.056842 restraints weight = 29531.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 4.02
r_work: 0.3066 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.375   7530  Z= 0.678
  Angle     :  0.963  22.547  10199  Z= 0.502
  Chirality :  0.050   0.445   1169
  Planarity :  0.006   0.077   1288
  Dihedral  :  3.715  51.615   1018
  Min Nonbonded Distance : 1.742

Molprobity Statistics.
  All-atom Clashscore : 37.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 20.57 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.27), residues: 915
  helix:  0.48 (0.25), residues: 407
  sheet: -1.70 (0.33), residues: 202
  loop : -1.46 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  87 
 HIS   0.009   0.001   HIS R 308 
 PHE   0.021   0.002   PHE A 343 
 TYR   0.011   0.002   TYR R  54 
 ARG   0.015   0.001   ARG G  26 

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.9289 (m-30) cc_final: 0.8990 (m-30)
REVERT: A   51 LYS cc_start: 0.9613 (mttp) cc_final: 0.9402 (tmmt)
REVERT: A  186 GLU cc_start: 0.8894 (tt0) cc_final: 0.8502 (tp30)
REVERT: A  198 MET cc_start: 0.9476 (ttm) cc_final: 0.9163 (ttp)
REVERT: B  219 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6744 (mpp80)
REVERT: B  280 SER cc_start: 0.9335 (OUTLIER) cc_final: 0.9032 (p)
REVERT: B  306 LYS cc_start: 0.8843 (mmtp) cc_final: 0.8633 (mmtm)
REVERT: G   28 LYS cc_start: 0.9466 (OUTLIER) cc_final: 0.9077 (mmmt)
REVERT: R  104 ASP cc_start: 0.7129 (m-30) cc_final: 0.6680 (m-30)
REVERT: R  136 PHE cc_start: 0.7520 (m-10) cc_final: 0.7006 (m-10)
REVERT: R  170 CYS cc_start: 0.8445 (p) cc_final: 0.8212 (p)
REVERT: R  224 VAL cc_start: 0.9618 (t) cc_final: 0.9393 (p)
REVERT: R  237 TYR cc_start: 0.7638 (m-10) cc_final: 0.7342 (m-10)
  outliers start: 13
  outliers final: 10
  residues processed: 105
  average time/residue: 1.1672
  time to fit residues: 129.9341
Evaluate side-chains
  107 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  274 LYS
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain G residue   12 ARG
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain R residue  129 THR
Chi-restraints excluded: chain R residue  133 VAL
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  308 HIS
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 76 optimal weight:    7.9990
   chunk 65 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 62 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.071832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.056865 restraints weight = 29826.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 4.04
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.375   7530  Z= 0.678
  Angle     :  0.963  22.547  10199  Z= 0.502
  Chirality :  0.050   0.445   1169
  Planarity :  0.006   0.077   1288
  Dihedral  :  3.715  51.615   1018
  Min Nonbonded Distance : 1.539

Molprobity Statistics.
  All-atom Clashscore : 38.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 20.69 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.27), residues: 915
  helix:  0.48 (0.25), residues: 407
  sheet: -1.70 (0.33), residues: 202
  loop : -1.46 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  87 
 HIS   0.009   0.001   HIS R 308 
 PHE   0.021   0.002   PHE A 343 
 TYR   0.011   0.002   TYR R  54 
 ARG   0.015   0.001   ARG G  26 

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.9236 (m-30) cc_final: 0.8911 (m-30)
REVERT: A  186 GLU cc_start: 0.8413 (tt0) cc_final: 0.8076 (tp30)
REVERT: A  198 MET cc_start: 0.9101 (ttm) cc_final: 0.8754 (ttp)
REVERT: B  219 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6445 (mpp80)
REVERT: B  280 SER cc_start: 0.9183 (OUTLIER) cc_final: 0.8833 (p)
REVERT: B  306 LYS cc_start: 0.8813 (mmtp) cc_final: 0.8587 (mmtm)
REVERT: G   28 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.8995 (mmmt)
REVERT: R  104 ASP cc_start: 0.6937 (m-30) cc_final: 0.6555 (m-30)
REVERT: R  170 CYS cc_start: 0.8481 (p) cc_final: 0.8234 (p)
REVERT: R  224 VAL cc_start: 0.9599 (t) cc_final: 0.9359 (p)
  outliers start: 13
  outliers final: 10
  residues processed: 102
  average time/residue: 1.1804
  time to fit residues: 127.7364
Evaluate side-chains
  106 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  274 LYS
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain G residue   12 ARG
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain R residue  129 THR
Chi-restraints excluded: chain R residue  133 VAL
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  308 HIS
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 67 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   chunk 63 optimal weight:    4.9990
   chunk 79 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.071279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.056498 restraints weight = 29510.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 4.00
r_work: 0.3060 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.233   7530  Z= 0.613
  Angle     :  1.044  26.312  10199  Z= 0.536
  Chirality :  0.049   0.302   1169
  Planarity :  0.007   0.108   1288
  Dihedral  :  3.806  50.112   1018
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 24.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 18.34 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.00 (0.27), residues: 915
  helix:  0.53 (0.25), residues: 407
  sheet: -1.61 (0.34), residues: 201
  loop : -1.45 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP X   3 
 HIS   0.015   0.002   HIS R 107 
 PHE   0.018   0.002   PHE A 343 
 TYR   0.011   0.002   TYR A  30 
 ARG   0.034   0.002   ARG B 219 

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.9300 (m-30) cc_final: 0.9005 (m-30)
REVERT: B  177 GLU cc_start: 0.9177 (tp30) cc_final: 0.8753 (tm-30)
REVERT: B  219 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7142 (mpp80)
REVERT: B  280 SER cc_start: 0.9335 (OUTLIER) cc_final: 0.9026 (p)
REVERT: B  306 LYS cc_start: 0.8842 (mmtp) cc_final: 0.8634 (mmtm)
REVERT: G   20 MET cc_start: 0.9590 (tpt) cc_final: 0.9103 (tpp)
REVERT: G   50 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8551 (mp)
REVERT: R  104 ASP cc_start: 0.7211 (m-30) cc_final: 0.6642 (m-30)
REVERT: R  136 PHE cc_start: 0.7395 (m-10) cc_final: 0.6838 (m-10)
REVERT: R  170 CYS cc_start: 0.8447 (p) cc_final: 0.8160 (p)
REVERT: R  264 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8367 (mp0)
  outliers start: 28
  outliers final: 14
  residues processed: 112
  average time/residue: 1.1519
  time to fit residues: 136.7662
Evaluate side-chains
  108 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain B residue   17 GLU
Chi-restraints excluded: chain B residue   24 ARG
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain R residue  129 THR
Chi-restraints excluded: chain R residue  180 LEU
Chi-restraints excluded: chain R residue  258 HIS
Chi-restraints excluded: chain R residue  308 HIS
Chi-restraints excluded: chain R residue  324 CYS
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 79 optimal weight:    0.2980
   chunk 6 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 258 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.071584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.056629 restraints weight = 29672.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 4.03
r_work: 0.3066 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.233   7530  Z= 0.613
  Angle     :  1.044  26.303  10199  Z= 0.536
  Chirality :  0.049   0.303   1169
  Planarity :  0.007   0.108   1288
  Dihedral  :  3.806  50.110   1018
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 32.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 20.57 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.00 (0.27), residues: 915
  helix:  0.53 (0.25), residues: 407
  sheet: -1.61 (0.34), residues: 201
  loop : -1.45 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP X   3 
 HIS   0.015   0.002   HIS R 107 
 PHE   0.018   0.002   PHE A 343 
 TYR   0.011   0.002   TYR A  30 
 ARG   0.034   0.002   ARG B 219 

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.9316 (m-30) cc_final: 0.9017 (m-30)
REVERT: B  177 GLU cc_start: 0.9158 (tp30) cc_final: 0.8734 (tm-30)
REVERT: B  219 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7160 (mpp80)
REVERT: B  280 SER cc_start: 0.9336 (OUTLIER) cc_final: 0.9027 (p)
REVERT: B  306 LYS cc_start: 0.8845 (mmtp) cc_final: 0.8622 (mmtm)
REVERT: G   20 MET cc_start: 0.9590 (tpt) cc_final: 0.9098 (tpp)
REVERT: G   50 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8552 (mp)
REVERT: R  104 ASP cc_start: 0.7093 (m-30) cc_final: 0.6648 (m-30)
REVERT: R  136 PHE cc_start: 0.7396 (m-10) cc_final: 0.6849 (m-10)
REVERT: R  170 CYS cc_start: 0.8450 (p) cc_final: 0.8170 (p)
REVERT: R  264 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8385 (mp0)
  outliers start: 16
  outliers final: 13
  residues processed: 101
  average time/residue: 1.1370
  time to fit residues: 121.7525
Evaluate side-chains
  107 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain B residue   17 GLU
Chi-restraints excluded: chain B residue   24 ARG
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain R residue  129 THR
Chi-restraints excluded: chain R residue  180 LEU
Chi-restraints excluded: chain R residue  308 HIS
Chi-restraints excluded: chain R residue  324 CYS
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 64 optimal weight:    0.6980
   chunk 57 optimal weight:    7.9990
   chunk 18 optimal weight:    0.5980
   chunk 80 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
** A  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 258 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.071505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.056665 restraints weight = 29708.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 4.01
r_work: 0.3067 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.233   7530  Z= 0.613
  Angle     :  1.044  26.303  10199  Z= 0.536
  Chirality :  0.049   0.303   1169
  Planarity :  0.007   0.108   1288
  Dihedral  :  3.806  50.110   1018
  Min Nonbonded Distance : 1.720

Molprobity Statistics.
  All-atom Clashscore : 32.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 20.69 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.00 (0.27), residues: 915
  helix:  0.53 (0.25), residues: 407
  sheet: -1.61 (0.34), residues: 201
  loop : -1.45 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP X   3 
 HIS   0.015   0.002   HIS R 107 
 PHE   0.018   0.002   PHE A 343 
 TYR   0.011   0.002   TYR A  30 
 ARG   0.034   0.002   ARG B 219 

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.9314 (m-30) cc_final: 0.9015 (m-30)
REVERT: B  177 GLU cc_start: 0.9169 (tp30) cc_final: 0.8746 (tm-30)
REVERT: B  219 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7147 (mpp80)
REVERT: B  280 SER cc_start: 0.9335 (OUTLIER) cc_final: 0.9025 (p)
REVERT: B  306 LYS cc_start: 0.8847 (mmtp) cc_final: 0.8622 (mmtm)
REVERT: G   20 MET cc_start: 0.9589 (tpt) cc_final: 0.9102 (tpp)
REVERT: G   50 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8553 (mp)
REVERT: R  104 ASP cc_start: 0.7095 (m-30) cc_final: 0.6649 (m-30)
REVERT: R  136 PHE cc_start: 0.7395 (m-10) cc_final: 0.6846 (m-10)
REVERT: R  170 CYS cc_start: 0.8447 (p) cc_final: 0.8166 (p)
REVERT: R  264 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8383 (mp0)
  outliers start: 16
  outliers final: 13
  residues processed: 101
  average time/residue: 1.1569
  time to fit residues: 123.9971
Evaluate side-chains
  107 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain B residue   17 GLU
Chi-restraints excluded: chain B residue   24 ARG
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain R residue  129 THR
Chi-restraints excluded: chain R residue  180 LEU
Chi-restraints excluded: chain R residue  308 HIS
Chi-restraints excluded: chain R residue  324 CYS
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 76 optimal weight:    8.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 258 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.071505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.056640 restraints weight = 30038.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 4.04
r_work: 0.3064 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.233   7530  Z= 0.613
  Angle     :  1.044  26.303  10199  Z= 0.536
  Chirality :  0.049   0.303   1169
  Planarity :  0.007   0.108   1288
  Dihedral  :  3.806  50.110   1018
  Min Nonbonded Distance : 1.720

Molprobity Statistics.
  All-atom Clashscore : 32.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 20.69 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.00 (0.27), residues: 915
  helix:  0.53 (0.25), residues: 407
  sheet: -1.61 (0.34), residues: 201
  loop : -1.45 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP X   3 
 HIS   0.015   0.002   HIS R 107 
 PHE   0.018   0.002   PHE A 343 
 TYR   0.011   0.002   TYR A  30 
 ARG   0.034   0.002   ARG B 219 

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.9313 (m-30) cc_final: 0.9013 (m-30)
REVERT: B  177 GLU cc_start: 0.9170 (tp30) cc_final: 0.8747 (tm-30)
REVERT: B  219 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7147 (mpp80)
REVERT: B  280 SER cc_start: 0.9336 (OUTLIER) cc_final: 0.9025 (p)
REVERT: B  306 LYS cc_start: 0.8844 (mmtp) cc_final: 0.8620 (mmtm)
REVERT: G   20 MET cc_start: 0.9591 (tpt) cc_final: 0.9101 (tpp)
REVERT: G   50 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8551 (mp)
REVERT: R  104 ASP cc_start: 0.7094 (m-30) cc_final: 0.6649 (m-30)
REVERT: R  136 PHE cc_start: 0.7392 (m-10) cc_final: 0.6845 (m-10)
REVERT: R  170 CYS cc_start: 0.8447 (p) cc_final: 0.8168 (p)
REVERT: R  264 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8383 (mp0)
  outliers start: 16
  outliers final: 13
  residues processed: 101
  average time/residue: 1.1653
  time to fit residues: 124.8424
Evaluate side-chains
  107 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain B residue   17 GLU
Chi-restraints excluded: chain B residue   24 ARG
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain R residue  129 THR
Chi-restraints excluded: chain R residue  180 LEU
Chi-restraints excluded: chain R residue  308 HIS
Chi-restraints excluded: chain R residue  324 CYS
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 41 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 258 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.071505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.056644 restraints weight = 30002.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 4.04
r_work: 0.3067 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.233   7530  Z= 0.613
  Angle     :  1.044  26.303  10199  Z= 0.536
  Chirality :  0.049   0.303   1169
  Planarity :  0.007   0.108   1288
  Dihedral  :  3.806  50.110   1018
  Min Nonbonded Distance : 1.720

Molprobity Statistics.
  All-atom Clashscore : 32.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 20.69 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.00 (0.27), residues: 915
  helix:  0.53 (0.25), residues: 407
  sheet: -1.61 (0.34), residues: 201
  loop : -1.45 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP X   3 
 HIS   0.015   0.002   HIS R 107 
 PHE   0.018   0.002   PHE A 343 
 TYR   0.011   0.002   TYR A  30 
 ARG   0.034   0.002   ARG B 219 

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.9317 (m-30) cc_final: 0.9017 (m-30)
REVERT: B  177 GLU cc_start: 0.9163 (tp30) cc_final: 0.8740 (tm-30)
REVERT: B  219 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7156 (mpp80)
REVERT: B  280 SER cc_start: 0.9335 (OUTLIER) cc_final: 0.9025 (p)
REVERT: B  306 LYS cc_start: 0.8849 (mmtp) cc_final: 0.8624 (mmtm)
REVERT: G   20 MET cc_start: 0.9593 (tpt) cc_final: 0.9102 (tpp)
REVERT: G   50 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8552 (mp)
REVERT: R  104 ASP cc_start: 0.7095 (m-30) cc_final: 0.6647 (m-30)
REVERT: R  136 PHE cc_start: 0.7390 (m-10) cc_final: 0.6845 (m-10)
REVERT: R  170 CYS cc_start: 0.8449 (p) cc_final: 0.8169 (p)
REVERT: R  264 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8386 (mp0)
  outliers start: 16
  outliers final: 13
  residues processed: 101
  average time/residue: 1.2014
  time to fit residues: 128.6619
Evaluate side-chains
  107 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain B residue   17 GLU
Chi-restraints excluded: chain B residue   24 ARG
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain R residue  129 THR
Chi-restraints excluded: chain R residue  180 LEU
Chi-restraints excluded: chain R residue  308 HIS
Chi-restraints excluded: chain R residue  324 CYS
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 80 optimal weight:    0.8980
   chunk 72 optimal weight:   50.0000
   chunk 0 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 67 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 258 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.071505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.056657 restraints weight = 29809.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 4.02
r_work: 0.3067 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.233   7530  Z= 0.613
  Angle     :  1.044  26.303  10199  Z= 0.536
  Chirality :  0.049   0.303   1169
  Planarity :  0.007   0.108   1288
  Dihedral  :  3.806  50.110   1018
  Min Nonbonded Distance : 1.720

Molprobity Statistics.
  All-atom Clashscore : 32.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 20.69 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.00 (0.27), residues: 915
  helix:  0.53 (0.25), residues: 407
  sheet: -1.61 (0.34), residues: 201
  loop : -1.45 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP X   3 
 HIS   0.015   0.002   HIS R 107 
 PHE   0.018   0.002   PHE A 343 
 TYR   0.011   0.002   TYR A  30 
 ARG   0.034   0.002   ARG B 219 

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.9314 (m-30) cc_final: 0.9015 (m-30)
REVERT: B  177 GLU cc_start: 0.9159 (tp30) cc_final: 0.8734 (tm-30)
REVERT: B  219 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7159 (mpp80)
REVERT: B  280 SER cc_start: 0.9337 (OUTLIER) cc_final: 0.9027 (p)
REVERT: B  306 LYS cc_start: 0.8846 (mmtp) cc_final: 0.8622 (mmtm)
REVERT: G   20 MET cc_start: 0.9591 (tpt) cc_final: 0.9099 (tpp)
REVERT: G   50 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8552 (mp)
REVERT: R  104 ASP cc_start: 0.7093 (m-30) cc_final: 0.6647 (m-30)
REVERT: R  136 PHE cc_start: 0.7395 (m-10) cc_final: 0.6850 (m-10)
REVERT: R  170 CYS cc_start: 0.8451 (p) cc_final: 0.8171 (p)
REVERT: R  264 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8388 (mp0)
  outliers start: 16
  outliers final: 13
  residues processed: 101
  average time/residue: 1.2398
  time to fit residues: 132.8577
Evaluate side-chains
  107 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain B residue   17 GLU
Chi-restraints excluded: chain B residue   24 ARG
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain R residue  129 THR
Chi-restraints excluded: chain R residue  180 LEU
Chi-restraints excluded: chain R residue  308 HIS
Chi-restraints excluded: chain R residue  324 CYS
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 72 optimal weight:   50.0000
   chunk 61 optimal weight:    8.9990
   chunk 46 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 258 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.071505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.056672 restraints weight = 29635.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 4.01
r_work: 0.3068 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.233   7530  Z= 0.613
  Angle     :  1.044  26.303  10199  Z= 0.536
  Chirality :  0.049   0.303   1169
  Planarity :  0.007   0.108   1288
  Dihedral  :  3.806  50.110   1018
  Min Nonbonded Distance : 1.720

Molprobity Statistics.
  All-atom Clashscore : 32.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 20.69 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.00 (0.27), residues: 915
  helix:  0.53 (0.25), residues: 407
  sheet: -1.61 (0.34), residues: 201
  loop : -1.45 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP X   3 
 HIS   0.015   0.002   HIS R 107 
 PHE   0.018   0.002   PHE A 343 
 TYR   0.011   0.002   TYR A  30 
 ARG   0.034   0.002   ARG B 219 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5511.51 seconds
wall clock time: 95 minutes 18.27 seconds (5718.27 seconds total)