Starting phenix.real_space_refine
on Wed Aug  5 12:43:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m1u_63583/08_2026/9m1u_63583.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m1u_63583/08_2026/9m1u_63583.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m1u_63583/08_2026/9m1u_63583.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m1u_63583/08_2026/9m1u_63583.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m1u_63583/08_2026/9m1u_63583.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m1u_63583/08_2026/9m1u_63583.cif"
  }
  resolution = 2.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.003 sd=   0.096
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      65      5.16       5
     C    6240      2.51       5
     N    1682      2.21       5
     O    1839      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9826
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1860
          Classifications: {'peptide': 228}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 2540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2540
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 62
          Unresolved non-hydrogen angles: 78
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 45
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 957
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "S"
      Number of atoms: 1730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1730
          Classifications: {'peptide': 228}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 9, 'TRANS': 218}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "R"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2295
          Classifications: {'peptide': 286}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 10, 'TRANS': 275}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "R"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'SIN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.06, per 1000 atoms: 0.21
  Number of scatterers: 9826
  At special positions: 0
  Unit cell: (88.33, 122.64, 130.67, 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      65     16.00
     O    1839      8.00
     N    1682      7.00
     C    6240      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 183 " distance=2.25

  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: 0.98
  Conformation dependent library (CDL) restraints added in 297.0 milliseconds
  

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2370

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 16 sheets defined
      36.6% alpha, 25.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 40
      removed outlier: 3.541A  pdb=" N   ALA A  19 " --> pdb=" O   GLU A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 233 through 239
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.558A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.522A  pdb=" N   ARG A 389 " --> pdb=" O   GLN A 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.598A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
    Processing helix  chain 'S' and resid 220 through 224
    Processing helix  chain 'R' and resid 29 through 60
      removed outlier: 4.119A  pdb=" N   LEU R  36 " --> pdb=" O   LYS R  32 " (cutoff:3.500A)
      Proline residue:  R  37  - end of helix
      Proline residue:  R  49  - end of helix
    Processing helix  chain 'R' and resid 66 through 95
      Proline residue:  R  87  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 141 through 145
      removed outlier: 3.508A  pdb=" N   HIS R 145 " --> pdb=" O   PHE R 142 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 166
      removed outlier: 3.707A  pdb=" N   ALA R 150 " --> pdb=" O   LYS R 146 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 167 through 170
    Processing helix  chain 'R' and resid 191 through 207
    Processing helix  chain 'R' and resid 207 through 228
    Processing helix  chain 'R' and resid 233 through 270
      Proline residue:  R 256  - end of helix
    Processing helix  chain 'R' and resid 273 through 293
      Proline residue:  R 289  - end of helix
    Processing helix  chain 'R' and resid 293 through 303
      removed outlier: 3.693A  pdb=" N   VAL R 303 " --> pdb=" O   LEU R 299 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 306 through 313
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.665A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 8.343A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.578A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 5.874A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.550A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.935A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.597A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.581A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.127A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.805A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12
      removed outlier: 4.256A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141
    Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148
      removed outlier: 6.114A  pdb=" N   VAL S 147 " --> pdb=" O   GLU S 246 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'R' and resid 174 through 175

    531 hydrogen bonds defined for protein.
    1452 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: 1.87

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1851
        1.33 -     1.45: 2570
        1.45 -     1.57: 5517
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 10028
  Sorted by residual:
  bond pdb=" C   ARG R 288 "
       pdb=" O   ARG R 288 "
    ideal  model  delta    sigma   weight residual
    1.244  1.206  0.038 1.00e-02 1.00e+04 1.44e+01
  bond pdb=" CA  ASP B 291 "
       pdb=" C   ASP B 291 "
    ideal  model  delta    sigma   weight residual
    1.523  1.476  0.047 1.80e-02 3.09e+03 6.94e+00
  bond pdb=" CA  ARG R 288 "
       pdb=" C   ARG R 288 "
    ideal  model  delta    sigma   weight residual
    1.520  1.544 -0.024 1.23e-02 6.61e+03 3.80e+00
  bond pdb=" C   ASP B 291 "
       pdb=" O   ASP B 291 "
    ideal  model  delta    sigma   weight residual
    1.236  1.208  0.028 1.47e-02 4.63e+03 3.68e+00
  bond pdb=" C   SER R 287 "
       pdb=" N   ARG R 288 "
    ideal  model  delta    sigma   weight residual
    1.332  1.304  0.028 1.50e-02 4.44e+03 3.58e+00
  ... (remaining 10023 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 13213
        1.44 -     2.87: 312
        2.87 -     4.31: 56
        4.31 -     5.75: 17
        5.75 -     7.19: 4
  Bond angle restraints: 13602
  Sorted by residual:
  angle pdb=" C   SER S  55 "
        pdb=" CA  SER S  55 "
        pdb=" CB  SER S  55 "
      ideal   model   delta    sigma   weight residual
     115.79  111.33    4.46 1.19e+00 7.06e-01 1.41e+01
  angle pdb=" N   GLY S 207 "
        pdb=" CA  GLY S 207 "
        pdb=" C   GLY S 207 "
      ideal   model   delta    sigma   weight residual
     110.96  114.78   -3.82 1.19e+00 7.06e-01 1.03e+01
  angle pdb=" C   ARG R 288 "
        pdb=" N   PRO R 289 "
        pdb=" CA  PRO R 289 "
      ideal   model   delta    sigma   weight residual
     119.56  116.64    2.92 1.02e+00 9.61e-01 8.18e+00
  angle pdb=" C   ASN R  28 "
        pdb=" N   ILE R  29 "
        pdb=" CA  ILE R  29 "
      ideal   model   delta    sigma   weight residual
     120.33  122.54   -2.21 8.00e-01 1.56e+00 7.65e+00
  angle pdb=" O   ASP B 290 "
        pdb=" C   ASP B 290 "
        pdb=" N   ASP B 291 "
      ideal   model   delta    sigma   weight residual
     122.46  119.07    3.39 1.38e+00 5.25e-01 6.03e+00
  ... (remaining 13597 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 5328
       17.63 -    35.27: 463
       35.27 -    52.90: 112
       52.90 -    70.53: 31
       70.53 -    88.17: 12
  Dihedral angle restraints: 5946
    sinusoidal: 2275
      harmonic: 3671
  Sorted by residual:
  dihedral pdb=" CA  GLN B  75 "
           pdb=" C   GLN B  75 "
           pdb=" N   ASP B  76 "
           pdb=" CA  ASP B  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.15   21.85     0      5.00e+00 4.00e-02 1.91e+01
  dihedral pdb=" CA  ARG S 191 "
           pdb=" C   ARG S 191 "
           pdb=" N   MET S 192 "
           pdb=" CA  MET S 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.54   20.46     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.47   19.53     0      5.00e+00 4.00e-02 1.53e+01
  ... (remaining 5943 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1377
       0.061 -    0.122: 158
       0.122 -    0.183: 20
       0.183 -    0.243: 1
       0.243 -    0.304: 1
  Chirality restraints: 1557
  Sorted by residual:
  chirality pdb=" CA  ASP B 291 "
            pdb=" N   ASP B 291 "
            pdb=" C   ASP B 291 "
            pdb=" CB  ASP B 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.31e+00
  chirality pdb=" CA  TYR A 391 "
            pdb=" N   TYR A 391 "
            pdb=" C   TYR A 391 "
            pdb=" CB  TYR A 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CA  ARG R 288 "
            pdb=" N   ARG R 288 "
            pdb=" C   ARG R 288 "
            pdb=" CB  ARG R 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.41e-01
  ... (remaining 1554 not shown)

  Planarity restraints: 1726
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 356 "   -0.137 9.50e-02 1.11e+02   6.14e-02 2.57e+00
        pdb=" NE  ARG A 356 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 356 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 356 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 356 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 166 "    0.027 5.00e-02 4.00e+02   3.98e-02 2.54e+00
        pdb=" N   PRO R 167 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO R 167 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO R 167 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 291 "    0.007 2.00e-02 2.50e+03   1.39e-02 1.94e+00
        pdb=" C   ASP B 291 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   ASP B 291 "    0.009 2.00e-02 2.50e+03
        pdb=" N   PHE B 292 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1723 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 955
        2.74 -     3.28: 9775
        3.28 -     3.82: 16806
        3.82 -     4.36: 20535
        4.36 -     4.90: 35989
  Nonbonded interactions: 84060
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 283 "
            pdb=" OG1 THR A 284 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   ASP B 195 "
            pdb=" OG1 THR B 196 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   THR B  86 "
            pdb=" OG1 THR B  87 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" NZ  LYS R  32 "
            pdb=" OE2 GLU R  97 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" NH2 ARG A 228 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.318 3.120
  ... (remaining 84055 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:             1.040
  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:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.840
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
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   0.221  10029  Z= 0.192
  Angle     :  0.574   7.843  13604  Z= 0.320
  Chirality :  0.042   0.304   1557
  Planarity :  0.004   0.061   1726
  Dihedral  : 15.120  88.165   3573
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 12.96 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.24), residues: 1244
  helix:  2.38 (0.26), residues: 396
  sheet: -0.07 (0.27), residues: 338
  loop :  0.35 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 356 
 TYR   0.011   0.001   TYR S 190 
 PHE   0.017   0.001   PHE R 170 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 114 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.16 (10028)
  covalent geometry    : angle       0.56957 /  0.32 (13602)
  SS BOND              : bond        0.22070 / 11.62 (    1)
  SS BOND              : angle       5.62674 /  2.97 (    2)
  hydrogen bonds       : bond        0.13097 /  8.68 (  524)
  hydrogen bonds       : angle       6.13142 /  4.28 ( 1452)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 235
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.7013 (mtpp) cc_final: 0.6714 (mttt)
REVERT: A   38 ARG cc_start: 0.7345 (tpt-90) cc_final: 0.7052 (tpp-160)
REVERT: A   54 SER cc_start: 0.7401 (m) cc_final: 0.7040 (p)
REVERT: A  211 LYS cc_start: 0.8316 (mttt) cc_final: 0.8071 (mttp)
REVERT: A  216 LYS cc_start: 0.7698 (mtpt) cc_final: 0.7487 (mttt)
REVERT: A  314 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6513 (mp0)
REVERT: A  370 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6864 (mt-10)
REVERT: B   23 LYS cc_start: 0.6829 (tttt) cc_final: 0.6549 (tppt)
REVERT: B   42 ARG cc_start: 0.7504 (tpt170) cc_final: 0.6818 (tmt170)
REVERT: B   44 GLN cc_start: 0.7640 (mt0) cc_final: 0.7416 (mt0)
REVERT: B   46 ARG cc_start: 0.7063 (mtp-110) cc_final: 0.6788 (mtp85)
REVERT: B   98 SER cc_start: 0.8292 (m) cc_final: 0.7587 (t)
REVERT: B  111 TYR cc_start: 0.8336 (m-80) cc_final: 0.7915 (m-80)
REVERT: B  134 ARG cc_start: 0.7422 (ptp-170) cc_final: 0.6325 (ptm-80)
REVERT: B  154 ASP cc_start: 0.7916 (m-30) cc_final: 0.7465 (m-30)
REVERT: B  172 GLU cc_start: 0.6719 (tt0) cc_final: 0.6462 (tt0)
REVERT: B  175 GLN cc_start: 0.7224 (mm110) cc_final: 0.6953 (mp-120)
REVERT: B  186 ASP cc_start: 0.7152 (m-30) cc_final: 0.6861 (m-30)
REVERT: B  219 ARG cc_start: 0.7098 (mtp85) cc_final: 0.6823 (mtp180)
REVERT: B  237 ASN cc_start: 0.6801 (t0) cc_final: 0.6566 (t0)
REVERT: G   42 GLU cc_start: 0.7133 (tt0) cc_final: 0.6489 (mt-10)
REVERT: N   46 GLU cc_start: 0.7423 (tt0) cc_final: 0.7004 (tm-30)
REVERT: N   83 MET cc_start: 0.7831 (mtp) cc_final: 0.7618 (mtp)
REVERT: S   73 ASP cc_start: 0.6795 (t70) cc_final: 0.6092 (p0)
REVERT: S   76 LYS cc_start: 0.7933 (mtpt) cc_final: 0.7266 (mppt)
REVERT: S   87 ARG cc_start: 0.5493 (mtm-85) cc_final: 0.4937 (mtm180)
REVERT: S   96 CYS cc_start: 0.8275 (t) cc_final: 0.7202 (p)
REVERT: S  160 ARG cc_start: 0.6519 (ttm110) cc_final: 0.6233 (mmm-85)
REVERT: S  230 MET cc_start: 0.8352 (ttp) cc_final: 0.8132 (ttp)
REVERT: R  240 ARG cc_start: 0.7106 (ttp80) cc_final: 0.6887 (mtp85)
  outliers start: 5
  outliers final: 0
  residues processed: 238
  average time/residue: 0.5285
  time to fit residues: 135.3861
Evaluate side-chains
  171 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 237 ASN
B 239 ASN
B 259 GLN
N  77 ASN
S 186 GLN
S 194 ASN
R  91 HIS
R 281 HIS
R 294 ASN
R 298 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.159951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.117810 restraints weight = 11399.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.86
r_work: 0.3261 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.1538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10029  Z= 0.122
  Angle     :  0.525   5.907  13604  Z= 0.285
  Chirality :  0.042   0.142   1557
  Planarity :  0.004   0.038   1726
  Dihedral  :  5.120  56.963   1375
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 15.02 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.24), residues: 1244
  helix:  2.73 (0.25), residues: 397
  sheet:  0.17 (0.27), residues: 326
  loop :  0.37 (0.28), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 333 
 TYR   0.020   0.001   TYR R  92 
 PHE   0.018   0.001   PHE A 212 
 TRP   0.015   0.001   TRP B 339 
 HIS   0.005   0.001   HIS R 281 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 (10028)
  covalent geometry    : angle       0.52489 /  0.28 (13602)
  SS BOND              : bond        0.00708 /  0.37 (    1)
  SS BOND              : angle       0.36301 /  0.21 (    2)
  hydrogen bonds       : bond        0.03970 /  2.55 (  524)
  hydrogen bonds       : angle       4.82680 /  3.40 ( 1452)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 183
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 ARG cc_start: 0.8205 (mtm-85) cc_final: 0.7545 (ttm-80)
REVERT: A   54 SER cc_start: 0.8400 (m) cc_final: 0.8128 (p)
REVERT: A  314 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7400 (mp0)
REVERT: B   17 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.6673 (tp40)
REVERT: B   23 LYS cc_start: 0.7622 (tttt) cc_final: 0.7296 (tppt)
REVERT: B   42 ARG cc_start: 0.7686 (tpt170) cc_final: 0.7363 (tmt170)
REVERT: B   98 SER cc_start: 0.8891 (m) cc_final: 0.8680 (t)
REVERT: B  134 ARG cc_start: 0.8411 (ptp-170) cc_final: 0.7877 (ptm-80)
REVERT: B  219 ARG cc_start: 0.8119 (mtp85) cc_final: 0.7917 (mtp180)
REVERT: B  256 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8204 (mtp180)
REVERT: G   42 GLU cc_start: 0.8018 (tt0) cc_final: 0.7480 (mt-10)
REVERT: N   53 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7789 (mp-120)
REVERT: N   83 MET cc_start: 0.9061 (mtp) cc_final: 0.8711 (mtp)
REVERT: S   65 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8122 (ttmt)
REVERT: S   73 ASP cc_start: 0.7817 (t70) cc_final: 0.7229 (p0)
REVERT: S   76 LYS cc_start: 0.8413 (mtpt) cc_final: 0.7808 (mppt)
REVERT: S   96 CYS cc_start: 0.8328 (t) cc_final: 0.8042 (p)
REVERT: S  159 CYS cc_start: 0.7487 (p) cc_final: 0.7282 (t)
REVERT: S  160 ARG cc_start: 0.6955 (ttm110) cc_final: 0.6616 (tpp-160)
REVERT: R  100 ILE cc_start: 0.8381 (pp) cc_final: 0.8141 (mp)
REVERT: R  200 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8366 (mm)
REVERT: R  240 ARG cc_start: 0.7360 (ttp80) cc_final: 0.6857 (ttp-110)
REVERT: R  241 ARG cc_start: 0.7470 (mtt90) cc_final: 0.7245 (mmt180)
  outliers start: 39
  outliers final: 11
  residues processed: 205
  average time/residue: 0.5114
  time to fit residues: 112.6329
Evaluate side-chains
  177 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 161
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   53 GLN
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   65 LYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   65 LYS
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  181 SER
Chi-restraints excluded: chain R residue  200 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 119 optimal weight:    0.9990
   chunk 121 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 115 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 72 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 24 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    1.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 279 ASN
A 292 ASN
A 392 ASN
N  77 ASN
S 186 GLN
R 294 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.158376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.115603 restraints weight = 11405.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 1.86
r_work: 0.3234 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10029  Z= 0.127
  Angle     :  0.515   5.830  13604  Z= 0.278
  Chirality :  0.042   0.138   1557
  Planarity :  0.004   0.029   1726
  Dihedral  :  5.069  56.796   1375
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 16.62 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.24), residues: 1244
  helix:  2.78 (0.25), residues: 391
  sheet:  0.09 (0.28), residues: 318
  loop :  0.27 (0.27), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 333 
 TYR   0.021   0.002   TYR R  92 
 PHE   0.015   0.001   PHE A 212 
 TRP   0.018   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 357 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 (10028)
  covalent geometry    : angle       0.51544 /  0.28 (13602)
  SS BOND              : bond        0.00131 /  0.07 (    1)
  SS BOND              : angle       0.47302 /  0.26 (    2)
  hydrogen bonds       : bond        0.03888 /  2.50 (  524)
  hydrogen bonds       : angle       4.61202 /  3.27 ( 1452)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 170
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7589 (ttm-80)
REVERT: A  314 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7378 (mp0)
REVERT: B   17 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6688 (tp40)
REVERT: B   23 LYS cc_start: 0.7710 (tttt) cc_final: 0.7366 (tppt)
REVERT: B   42 ARG cc_start: 0.7687 (tpt170) cc_final: 0.7410 (tmt170)
REVERT: B  134 ARG cc_start: 0.8468 (ptp-170) cc_final: 0.7917 (ptm-80)
REVERT: B  219 ARG cc_start: 0.8076 (mtp85) cc_final: 0.7850 (mtp180)
REVERT: B  256 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8173 (mtp180)
REVERT: G   42 GLU cc_start: 0.8087 (tt0) cc_final: 0.7552 (mt-10)
REVERT: N   83 MET cc_start: 0.9031 (mtp) cc_final: 0.8763 (mtp)
REVERT: S   87 ARG cc_start: 0.6052 (mtm-85) cc_final: 0.5551 (mtm180)
REVERT: S   96 CYS cc_start: 0.8351 (t) cc_final: 0.8084 (p)
REVERT: S  159 CYS cc_start: 0.7587 (OUTLIER) cc_final: 0.6710 (t)
REVERT: R  100 ILE cc_start: 0.8398 (pp) cc_final: 0.8172 (mp)
REVERT: R  106 CYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7206 (t)
REVERT: R  240 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6793 (ttp-110)
REVERT: R  241 ARG cc_start: 0.7536 (mtt90) cc_final: 0.7288 (mmt180)
  outliers start: 37
  outliers final: 15
  residues processed: 196
  average time/residue: 0.5116
  time to fit residues: 107.7993
Evaluate side-chains
  176 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 156
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   65 LYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  159 CYS
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  151 VAL
Chi-restraints excluded: chain R residue  181 SER
Chi-restraints excluded: chain R residue  226 THR
Chi-restraints excluded: chain R residue  240 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 90 optimal weight:    7.9990
   chunk 31 optimal weight:    4.9990
   chunk 118 optimal weight:    0.8980
   chunk 14 optimal weight:    0.2980
   chunk 93 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   chunk 67 optimal weight:    5.9990
   chunk 86 optimal weight:    7.9990
   chunk 39 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    2.4386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  77 ASN
S 186 GLN
** R  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 294 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.154585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.110874 restraints weight = 11530.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 1.88
r_work: 0.3165 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8737
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  10029  Z= 0.196
  Angle     :  0.570   6.839  13604  Z= 0.307
  Chirality :  0.044   0.149   1557
  Planarity :  0.004   0.038   1726
  Dihedral  :  5.374  59.828   1375
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 16.43 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.23), residues: 1244
  helix:  2.57 (0.24), residues: 390
  sheet:  0.07 (0.28), residues: 315
  loop :  0.18 (0.26), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 129 
 TYR   0.019   0.002   TYR R  92 
 PHE   0.018   0.002   PHE B 199 
 TRP   0.016   0.002   TRP A 234 
 HIS   0.008   0.001   HIS A 357 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00458 /  0.20 (10028)
  covalent geometry    : angle       0.57020 /  0.31 (13602)
  SS BOND              : bond        0.00157 /  0.08 (    1)
  SS BOND              : angle       0.42765 /  0.24 (    2)
  hydrogen bonds       : bond        0.04427 /  2.87 (  524)
  hydrogen bonds       : angle       4.75147 /  3.38 ( 1452)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 159
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.7659 (ttm-80)
REVERT: A  314 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7528 (mp0)
REVERT: B   17 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.6714 (tp40)
REVERT: B   23 LYS cc_start: 0.7793 (tttt) cc_final: 0.7370 (tppt)
REVERT: B  134 ARG cc_start: 0.8521 (ptp-170) cc_final: 0.7921 (ptm-80)
REVERT: B  256 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8196 (mtp180)
REVERT: B  304 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7852 (ttm170)
REVERT: G   42 GLU cc_start: 0.8142 (tt0) cc_final: 0.7610 (mt-10)
REVERT: N   83 MET cc_start: 0.8974 (mtp) cc_final: 0.8638 (mtp)
REVERT: S   87 ARG cc_start: 0.6082 (mtm-85) cc_final: 0.5653 (mtm180)
REVERT: S  141 THR cc_start: 0.7310 (t) cc_final: 0.6985 (m)
REVERT: S  159 CYS cc_start: 0.7212 (p) cc_final: 0.6631 (t)
REVERT: S  160 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.6113 (mpp-170)
  outliers start: 49
  outliers final: 22
  residues processed: 192
  average time/residue: 0.5544
  time to fit residues: 114.0573
Evaluate side-chains
  171 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 145
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   65 LYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  160 ARG
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  210 THR
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  151 VAL
Chi-restraints excluded: chain R residue  181 SER
Chi-restraints excluded: chain R residue  226 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 98 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 116 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 102 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 294 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.157470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.114445 restraints weight = 11421.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 1.86
r_work: 0.3218 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10029  Z= 0.120
  Angle     :  0.505   6.159  13604  Z= 0.273
  Chirality :  0.042   0.237   1557
  Planarity :  0.004   0.033   1726
  Dihedral  :  5.004  54.536   1375
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 18.50 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.23), residues: 1244
  helix:  2.70 (0.25), residues: 390
  sheet:  0.16 (0.28), residues: 322
  loop :  0.12 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 129 
 TYR   0.024   0.001   TYR R  92 
 PHE   0.017   0.001   PHE S  68 
 TRP   0.015   0.001   TRP A 234 
 HIS   0.005   0.001   HIS R 281 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.12 (10028)
  covalent geometry    : angle       0.50533 /  0.27 (13602)
  SS BOND              : bond        0.00163 /  0.09 (    1)
  SS BOND              : angle       0.40042 /  0.22 (    2)
  hydrogen bonds       : bond        0.03781 /  2.45 (  524)
  hydrogen bonds       : angle       4.56959 /  3.24 ( 1452)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 163
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.7605 (ttm-80)
REVERT: A  314 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7484 (mt-10)
REVERT: B   17 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.6736 (tp40)
REVERT: B   23 LYS cc_start: 0.7769 (tttt) cc_final: 0.7227 (tppt)
REVERT: B  134 ARG cc_start: 0.8498 (ptp-170) cc_final: 0.7941 (ptm-80)
REVERT: B  256 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8212 (mtp180)
REVERT: B  304 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7895 (ttm170)
REVERT: G   38 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7548 (mtm)
REVERT: G   42 GLU cc_start: 0.8112 (tt0) cc_final: 0.7653 (mt-10)
REVERT: N   83 MET cc_start: 0.8923 (mtp) cc_final: 0.8601 (mtp)
REVERT: S    3 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7191 (tp40)
REVERT: S   87 ARG cc_start: 0.6089 (mtm-85) cc_final: 0.5645 (mtm180)
REVERT: S   96 CYS cc_start: 0.8355 (t) cc_final: 0.8103 (p)
REVERT: S  141 THR cc_start: 0.7209 (t) cc_final: 0.6922 (m)
REVERT: S  159 CYS cc_start: 0.7120 (p) cc_final: 0.6473 (t)
REVERT: S  160 ARG cc_start: 0.6599 (mpp-170) cc_final: 0.6164 (mpp-170)
REVERT: R  106 CYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7079 (t)
REVERT: R  168 MET cc_start: 0.8525 (ttm) cc_final: 0.8038 (ttp)
REVERT: R  181 SER cc_start: 0.7512 (OUTLIER) cc_final: 0.6859 (p)
REVERT: R  240 ARG cc_start: 0.7709 (ttp80) cc_final: 0.7106 (ttp-110)
  outliers start: 40
  outliers final: 17
  residues processed: 193
  average time/residue: 0.5056
  time to fit residues: 105.0612
Evaluate side-chains
  176 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  181 SER
Chi-restraints excluded: chain R residue  195 ILE
Chi-restraints excluded: chain R residue  226 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 67 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   chunk 72 optimal weight:    9.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  77 ASN
S 186 GLN
** R  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 294 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.155893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.112676 restraints weight = 11428.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.86
r_work: 0.3191 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10029  Z= 0.152
  Angle     :  0.535   6.412  13604  Z= 0.287
  Chirality :  0.042   0.137   1557
  Planarity :  0.004   0.035   1726
  Dihedral  :  5.079  54.615   1375
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 18.97 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.23), residues: 1244
  helix:  2.64 (0.25), residues: 389
  sheet:  0.18 (0.28), residues: 322
  loop :  0.09 (0.26), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 129 
 TYR   0.027   0.002   TYR R  92 
 PHE   0.017   0.002   PHE S  68 
 TRP   0.014   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 357 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.15 (10028)
  covalent geometry    : angle       0.53494 /  0.29 (13602)
  SS BOND              : bond        0.00212 /  0.11 (    1)
  SS BOND              : angle       0.37314 /  0.20 (    2)
  hydrogen bonds       : bond        0.04035 /  2.62 (  524)
  hydrogen bonds       : angle       4.60863 /  3.28 ( 1452)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 154
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 ARG cc_start: 0.8327 (mtm-85) cc_final: 0.7604 (ttm-80)
REVERT: A  314 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7299 (mp0)
REVERT: A  317 ARG cc_start: 0.7702 (mtm-85) cc_final: 0.7476 (mtm-85)
REVERT: B   17 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.6779 (tp40)
REVERT: B   23 LYS cc_start: 0.7805 (tttt) cc_final: 0.7241 (tppt)
REVERT: B  134 ARG cc_start: 0.8523 (ptp-170) cc_final: 0.7971 (ptm-80)
REVERT: B  256 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8204 (mtp180)
REVERT: B  304 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7884 (ttm170)
REVERT: B  318 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8357 (mp)
REVERT: G   38 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7590 (mtm)
REVERT: G   42 GLU cc_start: 0.8104 (tt0) cc_final: 0.7682 (mt-10)
REVERT: N   83 MET cc_start: 0.8909 (mtp) cc_final: 0.8671 (mtp)
REVERT: S    3 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7161 (tp40)
REVERT: S   87 ARG cc_start: 0.6201 (mtm-85) cc_final: 0.5677 (mtp180)
REVERT: S   96 CYS cc_start: 0.8455 (t) cc_final: 0.8089 (p)
REVERT: S  141 THR cc_start: 0.7239 (t) cc_final: 0.6949 (m)
REVERT: S  159 CYS cc_start: 0.7200 (p) cc_final: 0.6558 (t)
REVERT: S  160 ARG cc_start: 0.6640 (mpp-170) cc_final: 0.6075 (mpp-170)
REVERT: S  171 ASN cc_start: 0.8806 (m-40) cc_final: 0.8568 (m110)
REVERT: R  106 CYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7146 (t)
  outliers start: 37
  outliers final: 23
  residues processed: 185
  average time/residue: 0.5562
  time to fit residues: 110.6206
Evaluate side-chains
  180 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 150
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  214 LEU
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain R residue   70 ILE
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  151 VAL
Chi-restraints excluded: chain R residue  181 SER
Chi-restraints excluded: chain R residue  226 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0070
   chunk 73 optimal weight:    3.9990
   chunk 55 optimal weight:    7.9990
   chunk 108 optimal weight:    9.9990
   chunk 33 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 111 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    1.7204

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  77 ASN
S  77 ASN
S 186 GLN
** R  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 294 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.155963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.112682 restraints weight = 11340.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.85
r_work: 0.3193 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10029  Z= 0.152
  Angle     :  0.543   6.716  13604  Z= 0.289
  Chirality :  0.043   0.230   1557
  Planarity :  0.004   0.036   1726
  Dihedral  :  5.070  53.381   1375
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 18.87 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.23), residues: 1244
  helix:  2.61 (0.25), residues: 389
  sheet:  0.19 (0.28), residues: 322
  loop :  0.05 (0.26), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 129 
 TYR   0.029   0.002   TYR R  92 
 PHE   0.016   0.002   PHE S  68 
 TRP   0.015   0.002   TRP A 234 
 HIS   0.006   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.15 (10028)
  covalent geometry    : angle       0.54288 /  0.29 (13602)
  SS BOND              : bond        0.00187 /  0.10 (    1)
  SS BOND              : angle       0.38157 /  0.21 (    2)
  hydrogen bonds       : bond        0.04048 /  2.63 (  524)
  hydrogen bonds       : angle       4.62333 /  3.30 ( 1452)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 156
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 ARG cc_start: 0.8329 (mtm-85) cc_final: 0.7618 (ttm-80)
REVERT: A  314 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7286 (mp0)
REVERT: B   10 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.6136 (tt0)
REVERT: B   17 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.6757 (tp40)
REVERT: B   23 LYS cc_start: 0.7812 (tttt) cc_final: 0.7268 (tppt)
REVERT: B  134 ARG cc_start: 0.8523 (ptp-170) cc_final: 0.7967 (ptm-80)
REVERT: B  256 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8197 (mtp180)
REVERT: B  304 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7909 (ttm170)
REVERT: B  318 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8351 (mp)
REVERT: G   38 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7584 (mtm)
REVERT: G   42 GLU cc_start: 0.8111 (tt0) cc_final: 0.7684 (mt-10)
REVERT: N   83 MET cc_start: 0.8867 (mtp) cc_final: 0.8564 (mtp)
REVERT: S    3 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7173 (tp40)
REVERT: S   87 ARG cc_start: 0.6158 (mtm-85) cc_final: 0.5650 (mtp180)
REVERT: S   96 CYS cc_start: 0.8423 (t) cc_final: 0.7993 (p)
REVERT: S  141 THR cc_start: 0.7212 (t) cc_final: 0.6922 (m)
REVERT: S  159 CYS cc_start: 0.7256 (p) cc_final: 0.6599 (t)
REVERT: S  160 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.6067 (mpp-170)
REVERT: R  181 SER cc_start: 0.7539 (OUTLIER) cc_final: 0.6857 (p)
REVERT: R  241 ARG cc_start: 0.7794 (mtt180) cc_final: 0.7399 (mmt180)
  outliers start: 40
  outliers final: 24
  residues processed: 187
  average time/residue: 0.5426
  time to fit residues: 108.8382
Evaluate side-chains
  184 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 151
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  160 ARG
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  214 LEU
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  151 VAL
Chi-restraints excluded: chain R residue  181 SER
Chi-restraints excluded: chain R residue  195 ILE
Chi-restraints excluded: chain R residue  226 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 75 optimal weight:    8.9990
   chunk 92 optimal weight:    9.9990
   chunk 7 optimal weight:    0.8980
   chunk 65 optimal weight:    8.9990
   chunk 80 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN
N  77 ASN
S  77 ASN
S 186 GLN
** R  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 294 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.155159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.110186 restraints weight = 11109.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 1.92
r_work: 0.3160 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8693
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10029  Z= 0.179
  Angle     :  0.569   7.007  13604  Z= 0.303
  Chirality :  0.044   0.188   1557
  Planarity :  0.004   0.038   1726
  Dihedral  :  5.205  54.595   1375
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 18.97 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.23), residues: 1244
  helix:  2.57 (0.25), residues: 388
  sheet:  0.16 (0.28), residues: 323
  loop :  0.03 (0.26), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 389 
 TYR   0.030   0.002   TYR R  92 
 PHE   0.016   0.002   PHE B 199 
 TRP   0.015   0.002   TRP A 234 
 HIS   0.007   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00419 /  0.18 (10028)
  covalent geometry    : angle       0.56928 /  0.30 (13602)
  SS BOND              : bond        0.00245 /  0.13 (    1)
  SS BOND              : angle       0.32413 /  0.18 (    2)
  hydrogen bonds       : bond        0.04239 /  2.75 (  524)
  hydrogen bonds       : angle       4.70815 /  3.37 ( 1452)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 150
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 ARG cc_start: 0.8330 (mtm-85) cc_final: 0.7576 (ttm-80)
REVERT: A  314 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7155 (mp0)
REVERT: B   10 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.6064 (tt0)
REVERT: B   17 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.6796 (tp40)
REVERT: B   23 LYS cc_start: 0.7782 (tttt) cc_final: 0.7311 (tppt)
REVERT: B  134 ARG cc_start: 0.8511 (ptp-170) cc_final: 0.7880 (ptm-80)
REVERT: B  256 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8155 (mtp180)
REVERT: B  304 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7913 (ttm170)
REVERT: B  318 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8431 (mp)
REVERT: G   42 GLU cc_start: 0.8044 (tt0) cc_final: 0.7641 (mt-10)
REVERT: N   83 MET cc_start: 0.8826 (mtp) cc_final: 0.8510 (mtp)
REVERT: S    3 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7083 (tp40)
REVERT: S   87 ARG cc_start: 0.5993 (mtm-85) cc_final: 0.5516 (mtp180)
REVERT: S   96 CYS cc_start: 0.8558 (t) cc_final: 0.7995 (p)
REVERT: S  141 THR cc_start: 0.7140 (t) cc_final: 0.6830 (m)
REVERT: S  159 CYS cc_start: 0.7272 (p) cc_final: 0.6585 (t)
REVERT: S  160 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6013 (mpp-170)
REVERT: R  181 SER cc_start: 0.7658 (OUTLIER) cc_final: 0.6952 (p)
REVERT: R  241 ARG cc_start: 0.7800 (mtt180) cc_final: 0.7387 (mmt180)
  outliers start: 42
  outliers final: 24
  residues processed: 184
  average time/residue: 0.5846
  time to fit residues: 115.3355
Evaluate side-chains
  181 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 149
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  160 ARG
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  151 VAL
Chi-restraints excluded: chain R residue  181 SER
Chi-restraints excluded: chain R residue  194 THR
Chi-restraints excluded: chain R residue  195 ILE
Chi-restraints excluded: chain R residue  226 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 109 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 98 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   chunk 111 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 39 optimal weight:    0.1980
   chunk 118 optimal weight:    0.3980
   chunk 34 optimal weight:    4.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  77 ASN
S  77 ASN
S 186 GLN
R 294 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.157333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.113561 restraints weight = 11230.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 1.89
r_work: 0.3207 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3094 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.2821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  10029  Z= 0.124
  Angle     :  0.528   6.827  13604  Z= 0.281
  Chirality :  0.042   0.185   1557
  Planarity :  0.004   0.034   1726
  Dihedral  :  4.905  48.980   1375
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 20.19 %
    Favored  : 76.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.23), residues: 1244
  helix:  2.63 (0.25), residues: 390
  sheet:  0.23 (0.28), residues: 322
  loop :  0.04 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 389 
 TYR   0.031   0.001   TYR R  92 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.015   0.001   TRP A 234 
 HIS   0.007   0.001   HIS R 281 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 (10028)
  covalent geometry    : angle       0.52757 /  0.28 (13602)
  SS BOND              : bond        0.00301 /  0.16 (    1)
  SS BOND              : angle       0.33848 /  0.18 (    2)
  hydrogen bonds       : bond        0.03768 /  2.45 (  524)
  hydrogen bonds       : angle       4.60702 /  3.30 ( 1452)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 156
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 ARG cc_start: 0.8268 (mtm-85) cc_final: 0.7532 (ttm-80)
REVERT: B   10 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.6085 (tt0)
REVERT: B   23 LYS cc_start: 0.7722 (tttt) cc_final: 0.7262 (tppt)
REVERT: B  134 ARG cc_start: 0.8503 (ptp-170) cc_final: 0.7882 (ptm-80)
REVERT: B  256 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8104 (mtp180)
REVERT: B  318 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8311 (mp)
REVERT: G   38 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7433 (mtm)
REVERT: G   42 GLU cc_start: 0.8048 (tt0) cc_final: 0.7614 (mt-10)
REVERT: S    3 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7080 (tp40)
REVERT: S   87 ARG cc_start: 0.5974 (mtm-85) cc_final: 0.5452 (mtp180)
REVERT: S   96 CYS cc_start: 0.8427 (t) cc_final: 0.7912 (p)
REVERT: S  141 THR cc_start: 0.7115 (t) cc_final: 0.6829 (m)
REVERT: S  159 CYS cc_start: 0.7113 (p) cc_final: 0.6432 (t)
REVERT: S  160 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.5959 (mpp-170)
REVERT: S  171 ASN cc_start: 0.8758 (m-40) cc_final: 0.8488 (m110)
REVERT: R  168 MET cc_start: 0.8504 (ttm) cc_final: 0.7959 (ttp)
  outliers start: 33
  outliers final: 20
  residues processed: 181
  average time/residue: 0.5575
  time to fit residues: 108.5174
Evaluate side-chains
  177 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 151
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  160 ARG
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  151 VAL
Chi-restraints excluded: chain R residue  181 SER
Chi-restraints excluded: chain R residue  194 THR
Chi-restraints excluded: chain R residue  226 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 85 optimal weight:    0.0570
   chunk 14 optimal weight:    0.0970
   chunk 87 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 95 optimal weight:    0.1980
   chunk 62 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   chunk 56 optimal weight:    6.9990
   chunk 35 optimal weight:    8.9990
   overall best weight:    0.4296

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 220 HIS
S  77 ASN
S 186 GLN
R  74 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.161561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.118843 restraints weight = 11143.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 1.87
r_work: 0.3270 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.073  10029  Z= 0.100
  Angle     :  0.499   6.662  13604  Z= 0.267
  Chirality :  0.040   0.141   1557
  Planarity :  0.004   0.031   1726
  Dihedral  :  4.520  39.117   1375
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 20.85 %
    Favored  : 76.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.23), residues: 1244
  helix:  2.70 (0.24), residues: 389
  sheet:  0.43 (0.29), residues: 308
  loop : -0.01 (0.26), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 129 
 TYR   0.031   0.001   TYR R  92 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.015   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00222 /  0.10 (10028)
  covalent geometry    : angle       0.49930 /  0.27 (13602)
  SS BOND              : bond        0.00431 /  0.23 (    1)
  SS BOND              : angle       0.44549 /  0.24 (    2)
  hydrogen bonds       : bond        0.03413 /  2.23 (  524)
  hydrogen bonds       : angle       4.47951 /  3.20 ( 1452)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 164
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7522 (ttm-80)
REVERT: B   23 LYS cc_start: 0.7765 (tttt) cc_final: 0.7169 (tppt)
REVERT: B  134 ARG cc_start: 0.8485 (ptp-170) cc_final: 0.8069 (ptt90)
REVERT: B  256 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8155 (mtp180)
REVERT: B  318 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8200 (mp)
REVERT: G   42 GLU cc_start: 0.8037 (tt0) cc_final: 0.7558 (mt-10)
REVERT: S    3 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7137 (tp40)
REVERT: S   87 ARG cc_start: 0.6035 (mtm-85) cc_final: 0.5455 (mtp180)
REVERT: S  141 THR cc_start: 0.7154 (t) cc_final: 0.6867 (m)
REVERT: S  159 CYS cc_start: 0.7048 (p) cc_final: 0.6347 (t)
REVERT: S  160 ARG cc_start: 0.6540 (mpp-170) cc_final: 0.6000 (mpp-170)
REVERT: S  186 GLN cc_start: 0.8458 (tt0) cc_final: 0.8192 (tt0)
REVERT: R  139 MET cc_start: 0.8216 (mmm) cc_final: 0.7577 (mtm)
REVERT: R  168 MET cc_start: 0.8473 (ttm) cc_final: 0.7955 (ttp)
  outliers start: 25
  outliers final: 14
  residues processed: 182
  average time/residue: 0.5293
  time to fit residues: 103.6655
Evaluate side-chains
  173 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 156
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  214 LEU
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  181 SER
Chi-restraints excluded: chain R residue  194 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 74 optimal weight:    9.9990
   chunk 71 optimal weight:    0.2980
   chunk 111 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 114 optimal weight:   10.0000
   chunk 38 optimal weight:    0.8980
   chunk 65 optimal weight:   10.0000
   chunk 88 optimal weight:    8.9990
   chunk 107 optimal weight:    4.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    2.6384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S  77 ASN
** R  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  91 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.155430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.111585 restraints weight = 11179.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 1.87
r_work: 0.3168 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8699
moved from start:          0.2916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077  10029  Z= 0.207
  Angle     :  0.608   8.791  13604  Z= 0.321
  Chirality :  0.045   0.231   1557
  Planarity :  0.004   0.047   1726
  Dihedral  :  5.135  48.663   1375
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 21.97 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.23), residues: 1244
  helix:  2.46 (0.24), residues: 389
  sheet:  0.17 (0.28), residues: 329
  loop :  0.02 (0.26), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 389 
 TYR   0.020   0.002   TYR R  58 
 PHE   0.023   0.002   PHE R 104 
 TRP   0.013   0.002   TRP A 281 
 HIS   0.007   0.002   HIS A 357 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00488 /  0.21 (10028)
  covalent geometry    : angle       0.60816 /  0.32 (13602)
  SS BOND              : bond        0.00244 /  0.13 (    1)
  SS BOND              : angle       0.39508 /  0.21 (    2)
  hydrogen bonds       : bond        0.04385 /  2.86 (  524)
  hydrogen bonds       : angle       4.77611 /  3.44 ( 1452)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4111.78 seconds
wall clock time: 70 minutes 38.33 seconds (4238.33 seconds total)