Starting phenix.real_space_refine
on Tue Mar 11 22:57:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xk8_33247/03_2025/7xk8_33247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xk8_33247/03_2025/7xk8_33247.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xk8_33247/03_2025/7xk8_33247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xk8_33247/03_2025/7xk8_33247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xk8_33247/03_2025/7xk8_33247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xk8_33247/03_2025/7xk8_33247.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    4352      2.51       5
     N    1151      2.21       5
     O    1247      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6796
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "P"
      Number of atoms: 202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 202
          Classifications: {'peptide': 25}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 22}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 2115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2115
          Classifications: {'peptide': 282}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 15, 'TRANS': 266}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 184
          Unresolved non-hydrogen angles: 230
          Unresolved non-hydrogen dihedrals: 162
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 7, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 99
    Chain: "A"
      Number of atoms: 1673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1673
          Classifications: {'peptide': 225}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 140
          Unresolved non-hydrogen angles: 165
          Unresolved non-hydrogen dihedrals: 117
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 77
    Chain: "B"
      Number of atoms: 2432
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2432
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 169
          Unresolved non-hydrogen angles: 204
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 7, 'ARG:plan': 10, 'ASN:plan1': 2, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 121
    Chain: "C"
      Number of atoms: 373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 373
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
  Time building chain proxies: 4.68, per 1000 atoms: 0.69
  Number of scatterers: 6796
  At special positions: 0
  Unit cell: (111.815, 127.49, 85.69, 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      46     16.00
     O    1247      8.00
     N    1151      7.00
     C    4352      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 119 " - pdb=" SG  CYS R 204 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.83
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1750

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 8 sheets defined
      43.2% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'R' and resid 45 through 72
      Proline residue:  R  54  - end of helix
    Processing helix  chain 'R' and resid 78 through 108
      Proline residue:  R 100  - end of helix
    Processing helix  chain 'R' and resid 115 through 150
    Processing helix  chain 'R' and resid 150 through 156
    Processing helix  chain 'R' and resid 157 through 159
      No H-bonds generated for 'chain 'R' and resid 157 through 159'
    Processing helix  chain 'R' and resid 160 through 184
      Proline residue:  R 180  - end of helix
    Processing helix  chain 'R' and resid 209 through 247
      removed outlier: 4.502A  pdb=" N   LEU R 227 " --> pdb=" O   LEU R 223 " (cutoff:3.500A)
      Proline residue:  R 228  - end of helix
    Processing helix  chain 'R' and resid 259 through 282
    Processing helix  chain 'R' and resid 282 through 292
      removed outlier: 3.987A  pdb=" N   ARG R 288 " --> pdb=" O   PHE R 284 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 299 through 328
      Proline residue:  R 324  - end of helix
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.993A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.624A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   LYS A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 271 through 281
      removed outlier: 4.172A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
    Processing helix  chain 'A' and resid 327 through 352
      removed outlier: 4.264A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 33
    Processing helix  chain 'C' and resid 12 through 21
    Processing helix  chain 'C' and resid 29 through 44
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.747A  pdb=" N   VAL A 185 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS A 197 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU A  36 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.146A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 4.224A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.832A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA B  73 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.863A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ASN B 125 " --> pdb=" O   ARG B 134 " (cutoff:3.500A)
      removed outlier: 4.473A  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: 4.271A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.861A  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: 6.988A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.875A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.672A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.802A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    368 hydrogen bonds defined for protein.
    1068 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: 1.94

  Time building geometry restraints manager: 2.18 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1099
        1.31 -     1.44: 1926
        1.44 -     1.56: 3855
        1.56 -     1.69: 0
        1.69 -     1.82: 62
  Bond restraints: 6942
  Sorted by residual:
  bond pdb=" CG  ASN P  25 "
       pdb=" ND2 ASN P  25 "
    ideal  model  delta    sigma   weight residual
    1.328  1.452 -0.124 2.10e-02 2.27e+03 3.46e+01
  bond pdb=" CG  ASN P  25 "
       pdb=" OD1 ASN P  25 "
    ideal  model  delta    sigma   weight residual
    1.231  1.185  0.046 1.90e-02 2.77e+03 5.92e+00
  bond pdb=" C   ASN P  25 "
       pdb=" O   ASN P  25 "
    ideal  model  delta    sigma   weight residual
    1.231  1.184  0.047 2.00e-02 2.50e+03 5.42e+00
  bond pdb=" C   SER P   9 "
       pdb=" N   PRO P  10 "
    ideal  model  delta    sigma   weight residual
    1.334  1.359 -0.025 2.34e-02 1.83e+03 1.12e+00
  bond pdb=" N   PRO R 193 "
       pdb=" CA  PRO R 193 "
    ideal  model  delta    sigma   weight residual
    1.469  1.475 -0.006 7.40e-03 1.83e+04 7.36e-01
  ... (remaining 6937 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 9231
        1.23 -     2.46: 184
        2.46 -     3.68: 41
        3.68 -     4.91: 11
        4.91 -     6.14: 8
  Bond angle restraints: 9475
  Sorted by residual:
  angle pdb=" N   ILE B  33 "
        pdb=" CA  ILE B  33 "
        pdb=" C   ILE B  33 "
      ideal   model   delta    sigma   weight residual
     112.96  109.56    3.40 1.00e+00 1.00e+00 1.16e+01
  angle pdb=" N   GLY R 186 "
        pdb=" CA  GLY R 186 "
        pdb=" C   GLY R 186 "
      ideal   model   delta    sigma   weight residual
     110.80  115.68   -4.88 1.71e+00 3.42e-01 8.15e+00
  angle pdb=" OD1 ASN P  25 "
        pdb=" CG  ASN P  25 "
        pdb=" ND2 ASN P  25 "
      ideal   model   delta    sigma   weight residual
     122.60  119.99    2.61 1.00e+00 1.00e+00 6.82e+00
  angle pdb=" N   THR B 196 "
        pdb=" CA  THR B 196 "
        pdb=" CB  THR B 196 "
      ideal   model   delta    sigma   weight residual
     113.65  110.02    3.63 1.47e+00 4.63e-01 6.11e+00
  angle pdb=" CB  ASN P  25 "
        pdb=" CG  ASN P  25 "
        pdb=" ND2 ASN P  25 "
      ideal   model   delta    sigma   weight residual
     116.40  120.02   -3.62 1.50e+00 4.44e-01 5.81e+00
  ... (remaining 9470 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.57: 3698
       15.57 -    31.14: 291
       31.14 -    46.70: 57
       46.70 -    62.27: 7
       62.27 -    77.84: 1
  Dihedral angle restraints: 4054
    sinusoidal: 1361
      harmonic: 2693
  Sorted by residual:
  dihedral pdb=" CA  PHE R 189 "
           pdb=" C   PHE R 189 "
           pdb=" N   HIS R 190 "
           pdb=" CA  HIS R 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.50   19.50     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CB  CYS R 119 "
           pdb=" SG  CYS R 119 "
           pdb=" SG  CYS R 204 "
           pdb=" CB  CYS R 204 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   65.34   27.66     1      1.00e+01 1.00e-02 1.10e+01
  dihedral pdb=" CA  ASP B  38 "
           pdb=" CB  ASP B  38 "
           pdb=" CG  ASP B  38 "
           pdb=" OD1 ASP B  38 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.44   53.44     1      2.00e+01 2.50e-03 9.71e+00
  ... (remaining 4051 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 756
       0.030 -    0.059: 243
       0.059 -    0.089: 79
       0.089 -    0.119: 44
       0.119 -    0.149: 3
  Chirality restraints: 1125
  Sorted by residual:
  chirality pdb=" CA  THR B 164 "
            pdb=" N   THR B 164 "
            pdb=" C   THR B 164 "
            pdb=" CB  THR B 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.52e-01
  chirality pdb=" CA  ILE R 187 "
            pdb=" N   ILE R 187 "
            pdb=" C   ILE R 187 "
            pdb=" CB  ILE R 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.35e-01
  chirality pdb=" CB  ILE R 184 "
            pdb=" CA  ILE R 184 "
            pdb=" CG1 ILE R 184 "
            pdb=" CG2 ILE R 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.28e-01
  ... (remaining 1122 not shown)

  Planarity restraints: 1203
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R  78 "   -0.019 5.00e-02 4.00e+02   2.88e-02 1.33e+00
        pdb=" N   PRO R  79 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO R  79 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO R  79 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA R 282 "    0.018 5.00e-02 4.00e+02   2.64e-02 1.12e+00
        pdb=" N   PRO R 283 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO R 283 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO R 283 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.015 5.00e-02 4.00e+02   2.26e-02 8.20e-01
        pdb=" N   PRO B 236 "   -0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.013 5.00e-02 4.00e+02
  ... (remaining 1200 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1396
        2.78 -     3.31: 6603
        3.31 -     3.84: 11498
        3.84 -     4.37: 12427
        4.37 -     4.90: 22105
  Nonbonded interactions: 54029
  Sorted by model distance:
  nonbonded pdb=" O   LEU R 289 "
            pdb=" OG  SER R 292 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OG1 THR R  78 "
            pdb=" OD1 ASP A 350 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASN B 110 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.306 3.040
  ... (remaining 54024 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:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.160
  Find NCS groups from input model:        0.070
  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:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6270
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.124   6942  Z= 0.142
  Angle     :  0.479   6.142   9475  Z= 0.271
  Chirality :  0.038   0.149   1125
  Planarity :  0.003   0.029   1203
  Dihedral  : 11.624  77.838   2301
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.25), residues: 907
  helix:  0.38 (0.24), residues: 371
  sheet: -0.45 (0.38), residues: 154
  loop : -2.23 (0.26), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP B  99 
 HIS   0.003   0.000   HIS R 285 
 PHE   0.010   0.001   PHE R 291 
 TYR   0.004   0.001   TYR B 289 
 ARG   0.001   0.000   ARG B 251 

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  127 GLU cc_start: 0.6422 (tp30) cc_final: 0.6077 (tp30)
REVERT: R  333 ARG cc_start: 0.4321 (pmt170) cc_final: 0.3932 (tpp-160)
REVERT: A    9 ASP cc_start: 0.7360 (t70) cc_final: 0.6993 (t0)
REVERT: B  188 MET cc_start: 0.7046 (mmm) cc_final: 0.6843 (mmm)
REVERT: C   62 ARG cc_start: 0.6621 (mtm-85) cc_final: 0.6392 (mtm110)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.2193
  time to fit residues: 45.1195
Evaluate side-chains
  99 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.0870
   chunk 68 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.9560

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

Flipped N/Q/H residues before XYZ refinement:
R  43 HIS
R 285 HIS
A  57 HIS
A 294 ASN
A 304 GLN
A 347 ASN
B 340 ASN
C  18 GLN
C  44 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4728 r_free = 0.4728 target = 0.213468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.171568 restraints weight = 7545.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.4329 rms_B_bonded: 3.24
r_work: 0.3975 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6942  Z= 0.235
  Angle     :  0.592   7.509   9475  Z= 0.305
  Chirality :  0.042   0.237   1125
  Planarity :  0.003   0.028   1203
  Dihedral  :  3.657  29.105    978
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.93 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.27), residues: 907
  helix:  1.56 (0.26), residues: 373
  sheet: -0.41 (0.39), residues: 145
  loop : -1.72 (0.28), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 169 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.023   0.002   PHE R 316 
 TYR   0.019   0.002   TYR R 213 
 ARG   0.005   0.001   ARG R 288 

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
REVERT: R  104 TYR cc_start: 0.3858 (m-80) cc_final: 0.3416 (m-80)
REVERT: R  333 ARG cc_start: 0.5062 (pmt170) cc_final: 0.3716 (tpp-160)
REVERT: A    9 ASP cc_start: 0.7272 (t70) cc_final: 0.6918 (t0)
REVERT: A   52 GLN cc_start: 0.6988 (pp30) cc_final: 0.6244 (pp30)
REVERT: A  247 MET cc_start: 0.7655 (mtm) cc_final: 0.7453 (ptp)
REVERT: C   62 ARG cc_start: 0.6796 (mtm-85) cc_final: 0.6316 (mtm110)
  outliers start: 15
  outliers final: 7
  residues processed: 128
  average time/residue: 0.1889
  time to fit residues: 32.0342
Evaluate side-chains
  109 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  189 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 62 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 30 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 78 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
R 285 HIS
A 294 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.210101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.167866 restraints weight = 7721.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.4280 rms_B_bonded: 3.20
r_work: 0.3931 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6942  Z= 0.217
  Angle     :  0.569   6.916   9475  Z= 0.291
  Chirality :  0.041   0.177   1125
  Planarity :  0.003   0.031   1203
  Dihedral  :  3.814  36.247    978
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 17.61 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.27), residues: 907
  helix:  1.90 (0.27), residues: 376
  sheet: -0.50 (0.40), residues: 146
  loop : -1.45 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.017   0.001   PHE R 284 
 TYR   0.016   0.001   TYR R 213 
 ARG   0.007   0.001   ARG B  49 

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
REVERT: R  104 TYR cc_start: 0.4076 (m-80) cc_final: 0.3622 (m-80)
REVERT: R  333 ARG cc_start: 0.4867 (pmt170) cc_final: 0.3655 (tpp-160)
REVERT: A    9 ASP cc_start: 0.7245 (t70) cc_final: 0.6910 (t0)
REVERT: C   62 ARG cc_start: 0.6779 (mtm-85) cc_final: 0.6462 (mtm110)
  outliers start: 24
  outliers final: 17
  residues processed: 131
  average time/residue: 0.1812
  time to fit residues: 31.9061
Evaluate side-chains
  119 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   82 TYR
Chi-restraints excluded: chain R residue  220 THR
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  311 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 83 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 68 optimal weight:    2.9990
   chunk 54 optimal weight:   20.0000
   chunk 38 optimal weight:    0.1980
   chunk 0 optimal weight:   20.0000
   chunk 71 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
R 285 HIS
A 294 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.200345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.144045 restraints weight = 7827.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3995 rms_B_bonded: 2.39
r_work: 0.3858 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073   6942  Z= 0.366
  Angle     :  0.659   8.847   9475  Z= 0.338
  Chirality :  0.044   0.172   1125
  Planarity :  0.004   0.036   1203
  Dihedral  :  4.437  42.886    978
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 20.30 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.28), residues: 907
  helix:  1.86 (0.26), residues: 376
  sheet: -0.69 (0.38), residues: 175
  loop : -1.48 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  99 
 HIS   0.005   0.002   HIS R 285 
 PHE   0.019   0.002   PHE R 316 
 TYR   0.011   0.002   TYR R 225 
 ARG   0.005   0.001   ARG B  49 

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.704 
Fit side-chains
REVERT: R  169 ILE cc_start: 0.4568 (OUTLIER) cc_final: 0.4262 (tp)
REVERT: R  239 MET cc_start: 0.5472 (mtp) cc_final: 0.5159 (ttm)
REVERT: R  333 ARG cc_start: 0.4860 (pmt170) cc_final: 0.3528 (tmt170)
REVERT: A  247 MET cc_start: 0.7738 (mtp) cc_final: 0.7517 (ptm)
  outliers start: 33
  outliers final: 22
  residues processed: 133
  average time/residue: 0.1703
  time to fit residues: 31.2972
Evaluate side-chains
  123 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  177 PHE
Chi-restraints excluded: chain R residue  182 THR
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  311 VAL
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  294 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 64 optimal weight:    0.1980
   chunk 8 optimal weight:    9.9990
   chunk 15 optimal weight:    0.0000
   chunk 58 optimal weight:    0.8980
   chunk 89 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
R 285 HIS
A 294 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4659 r_free = 0.4659 target = 0.206523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.149608 restraints weight = 7605.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 2.56
r_work: 0.3913 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6947
moved from start:          0.3218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6942  Z= 0.181
  Angle     :  0.560   8.098   9475  Z= 0.286
  Chirality :  0.041   0.144   1125
  Planarity :  0.003   0.034   1203
  Dihedral  :  4.046  40.928    978
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 22.69 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.28), residues: 907
  helix:  2.07 (0.27), residues: 377
  sheet: -0.49 (0.42), residues: 150
  loop : -1.40 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.005   0.001   HIS R 285 
 PHE   0.019   0.001   PHE B 199 
 TYR   0.017   0.001   TYR R 120 
 ARG   0.003   0.000   ARG A  15 

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 117
  time to evaluate  : 0.754 
Fit side-chains
REVERT: R   49 SER cc_start: 0.5223 (t) cc_final: 0.4583 (p)
REVERT: R  210 MET cc_start: 0.3705 (tpp) cc_final: 0.3241 (tpp)
REVERT: R  239 MET cc_start: 0.5747 (mtp) cc_final: 0.5451 (ttm)
REVERT: R  333 ARG cc_start: 0.4790 (pmt170) cc_final: 0.3498 (tmt170)
REVERT: A  197 LYS cc_start: 0.8448 (ptpt) cc_final: 0.8181 (ptmt)
REVERT: A  247 MET cc_start: 0.7570 (mtp) cc_final: 0.7368 (ptm)
REVERT: B  340 ASN cc_start: 0.5909 (t0) cc_final: 0.5687 (t0)
  outliers start: 29
  outliers final: 17
  residues processed: 135
  average time/residue: 0.1597
  time to fit residues: 30.0241
Evaluate side-chains
  121 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   82 TYR
Chi-restraints excluded: chain R residue  177 PHE
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  311 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  285 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0770
   chunk 15 optimal weight:   10.0000
   chunk 84 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 12 optimal weight:    9.9990
   chunk 58 optimal weight:    0.9980
   chunk 86 optimal weight:   30.0000
   chunk 79 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.205523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.148026 restraints weight = 7719.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.4054 rms_B_bonded: 2.61
r_work: 0.3908 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.3334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6942  Z= 0.203
  Angle     :  0.592  11.795   9475  Z= 0.296
  Chirality :  0.042   0.294   1125
  Planarity :  0.003   0.032   1203
  Dihedral  :  4.012  38.690    978
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 24.03 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.28), residues: 907
  helix:  2.20 (0.26), residues: 376
  sheet: -0.55 (0.41), residues: 148
  loop : -1.39 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.019   0.001   PHE R 316 
 TYR   0.010   0.001   TYR R 225 
 ARG   0.003   0.000   ARG B  49 

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 111
  time to evaluate  : 0.785 
Fit side-chains
REVERT: R  210 MET cc_start: 0.3805 (tpp) cc_final: 0.3353 (tpp)
REVERT: R  239 MET cc_start: 0.5614 (mtp) cc_final: 0.5297 (ttm)
REVERT: R  333 ARG cc_start: 0.4830 (pmt170) cc_final: 0.3495 (tmt170)
REVERT: A  197 LYS cc_start: 0.8466 (ptpt) cc_final: 0.8214 (ptmt)
  outliers start: 32
  outliers final: 21
  residues processed: 130
  average time/residue: 0.1660
  time to fit residues: 30.0905
Evaluate side-chains
  121 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  177 PHE
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  311 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 77 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 86 optimal weight:   20.0000
   chunk 51 optimal weight:    0.9980
   chunk 80 optimal weight:    0.8980
   chunk 14 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
R 285 HIS
A 294 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4642 r_free = 0.4642 target = 0.205137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.162131 restraints weight = 7634.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.4219 rms_B_bonded: 3.12
r_work: 0.3872 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6984
moved from start:          0.3462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6942  Z= 0.224
  Angle     :  0.593   8.994   9475  Z= 0.300
  Chirality :  0.042   0.286   1125
  Planarity :  0.003   0.033   1203
  Dihedral  :  4.029  39.787    978
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 24.63 %
    Favored  : 70.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.27), residues: 907
  helix:  2.20 (0.26), residues: 375
  sheet: -1.03 (0.38), residues: 160
  loop : -1.31 (0.29), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.007   0.001   HIS R 285 
 PHE   0.020   0.001   PHE R 316 
 TYR   0.013   0.001   TYR R 120 
 ARG   0.004   0.000   ARG A  15 

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 108
  time to evaluate  : 0.815 
Fit side-chains
REVERT: R   84 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5934 (mp)
REVERT: R  210 MET cc_start: 0.3847 (tpp) cc_final: 0.3380 (tpp)
REVERT: R  333 ARG cc_start: 0.4729 (pmt170) cc_final: 0.3440 (tmt170)
  outliers start: 34
  outliers final: 27
  residues processed: 129
  average time/residue: 0.1624
  time to fit residues: 29.3383
Evaluate side-chains
  131 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   84 LEU
Chi-restraints excluded: chain R residue  177 PHE
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  311 VAL
Chi-restraints excluded: chain R residue  322 VAL
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 54 optimal weight:   20.0000
   chunk 36 optimal weight:    8.9990
   chunk 44 optimal weight:    6.9990
   chunk 20 optimal weight:    0.0570
   chunk 14 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0970
   chunk 72 optimal weight:    2.9990
   chunk 15 optimal weight:    0.3980
   overall best weight:    1.1100

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.203577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.160548 restraints weight = 7673.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.4188 rms_B_bonded: 3.11
r_work: 0.3833 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6942  Z= 0.257
  Angle     :  0.620  11.089   9475  Z= 0.312
  Chirality :  0.043   0.280   1125
  Planarity :  0.003   0.034   1203
  Dihedral  :  4.117  40.683    978
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 24.03 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.27), residues: 907
  helix:  2.07 (0.26), residues: 378
  sheet: -0.99 (0.37), residues: 170
  loop : -1.33 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.032   0.002   PHE R 316 
 TYR   0.013   0.001   TYR R 120 
 ARG   0.003   0.000   ARG A  15 

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 108
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
REVERT: R   84 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5873 (mp)
REVERT: R  210 MET cc_start: 0.3951 (tpp) cc_final: 0.3261 (tpp)
REVERT: R  333 ARG cc_start: 0.4859 (pmt170) cc_final: 0.3467 (tmt170)
  outliers start: 40
  outliers final: 29
  residues processed: 131
  average time/residue: 0.1606
  time to fit residues: 29.7154
Evaluate side-chains
  135 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   84 LEU
Chi-restraints excluded: chain R residue  177 PHE
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  311 VAL
Chi-restraints excluded: chain R residue  322 VAL
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 5 optimal weight:    0.4980
   chunk 1 optimal weight:    5.9990
   chunk 82 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 22 optimal weight:   20.0000
   chunk 70 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.203671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.158893 restraints weight = 7637.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.4154 rms_B_bonded: 3.23
r_work: 0.3816 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.3743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6942  Z= 0.251
  Angle     :  0.626   9.897   9475  Z= 0.317
  Chirality :  0.043   0.279   1125
  Planarity :  0.004   0.033   1203
  Dihedral  :  4.126  40.664    978
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  5.52 %
    Allowed  : 24.63 %
    Favored  : 69.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.27), residues: 907
  helix:  2.06 (0.26), residues: 377
  sheet: -1.17 (0.38), residues: 167
  loop : -1.32 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.031   0.001   PHE R 316 
 TYR   0.031   0.001   TYR R 120 
 ARG   0.003   0.000   ARG A  15 

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 107
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
REVERT: R   84 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5948 (mp)
REVERT: R  169 ILE cc_start: 0.4869 (OUTLIER) cc_final: 0.4595 (tp)
REVERT: R  210 MET cc_start: 0.4007 (tpp) cc_final: 0.3373 (tpp)
REVERT: R  333 ARG cc_start: 0.4853 (pmt170) cc_final: 0.3426 (tmt170)
  outliers start: 37
  outliers final: 30
  residues processed: 130
  average time/residue: 0.1505
  time to fit residues: 27.5867
Evaluate side-chains
  138 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   84 LEU
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  177 PHE
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  242 ARG
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  311 VAL
Chi-restraints excluded: chain R residue  322 VAL
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0770
   chunk 31 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 40 optimal weight:    0.2980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.206561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.150065 restraints weight = 7633.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.4067 rms_B_bonded: 2.56
r_work: 0.3921 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6946
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6942  Z= 0.192
  Angle     :  0.611   9.380   9475  Z= 0.307
  Chirality :  0.042   0.279   1125
  Planarity :  0.003   0.033   1203
  Dihedral  :  4.022  40.623    978
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 25.67 %
    Favored  : 69.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.28), residues: 907
  helix:  2.11 (0.26), residues: 377
  sheet: -0.97 (0.39), residues: 163
  loop : -1.29 (0.30), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.029   0.001   PHE R 316 
 TYR   0.031   0.001   TYR R 120 
 ARG   0.003   0.000   ARG A  15 

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 112
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
REVERT: R   84 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5873 (mp)
REVERT: R  169 ILE cc_start: 0.4836 (OUTLIER) cc_final: 0.4575 (tp)
REVERT: R  210 MET cc_start: 0.4074 (tpp) cc_final: 0.3496 (tpp)
REVERT: R  333 ARG cc_start: 0.4828 (pmt170) cc_final: 0.3406 (tmt170)
REVERT: A  197 LYS cc_start: 0.8662 (ptpt) cc_final: 0.8318 (ptmt)
  outliers start: 34
  outliers final: 29
  residues processed: 134
  average time/residue: 0.1735
  time to fit residues: 33.7040
Evaluate side-chains
  139 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 108
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   84 LEU
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  177 PHE
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  242 ARG
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  311 VAL
Chi-restraints excluded: chain R residue  322 VAL
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 53 optimal weight:   20.0000
   chunk 57 optimal weight:    0.6980
   chunk 86 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 81 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 5 optimal weight:    7.9990
   chunk 9 optimal weight:    8.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4645 r_free = 0.4645 target = 0.205593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.161307 restraints weight = 7653.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.4202 rms_B_bonded: 3.21
r_work: 0.3872 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.3778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6942  Z= 0.215
  Angle     :  0.624  10.101   9475  Z= 0.313
  Chirality :  0.043   0.280   1125
  Planarity :  0.003   0.033   1203
  Dihedral  :  4.047  40.212    978
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 25.97 %
    Favored  : 69.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.28), residues: 907
  helix:  2.12 (0.26), residues: 377
  sheet: -1.10 (0.39), residues: 162
  loop : -1.30 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.031   0.001   PHE R 316 
 TYR   0.032   0.001   TYR R 120 
 ARG   0.003   0.000   ARG A  15 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4775.31 seconds
wall clock time: 82 minutes 8.81 seconds (4928.81 seconds total)