Starting phenix.real_space_refine
on Wed Mar 12 04:16:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iq6_35658/03_2025/8iq6_35658.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iq6_35658/03_2025/8iq6_35658.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iq6_35658/03_2025/8iq6_35658.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iq6_35658/03_2025/8iq6_35658.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iq6_35658/03_2025/8iq6_35658.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iq6_35658/03_2025/8iq6_35658.cif"
  }
  resolution = 3.4
  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=   0.066
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      52      5.16       5
     C    4541      2.51       5
     N    1203      2.21       5
     O    1263      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 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: 7059
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1560
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 3, 'TRANS': 197}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 115
          Unresolved non-hydrogen angles: 136
          Unresolved non-hydrogen dihedrals: 94
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 7, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 82
    Chain: "B"
      Number of atoms: 2342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2342
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 52}
          Link IDs: {'PTRANS': 5, 'TRANS': 323}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 187
          Unresolved non-hydrogen angles: 230
          Unresolved non-hydrogen dihedrals: 146
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 142
    Chain: "G"
      Number of atoms: 238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 238
          Classifications: {'peptide': 36}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 1, 'TRANS': 34}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "N"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 845
          Classifications: {'peptide': 114}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 109}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "R"
      Number of atoms: 2046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2046
          Classifications: {'peptide': 274}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 5, 'TRANS': 268}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 123
          Unresolved non-hydrogen angles: 153
          Unresolved non-hydrogen dihedrals: 104
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 77
    Chain: "R"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'7WT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.39, per 1000 atoms: 0.62
  Number of scatterers: 7059
  At special positions: 0
  Unit cell: (71.3635, 97.7131, 125.161, 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      52     16.00
     O    1263      8.00
     N    1203      7.00
     C    4541      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 108 " - pdb=" SG  CYS R 186 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.19
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1794

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 11 sheets defined
      41.3% alpha, 21.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 38
      removed outlier: 3.616A  pdb=" N   GLU A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.583A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 293 through 302
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.511A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 352
      removed outlier: 3.782A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 392
    Processing helix  chain 'B' and resid 8 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 16 through 23
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.616A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'N' and resid 62 through 65
      removed outlier: 3.777A  pdb=" N   LYS N  65 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 62 through 65'
    Processing helix  chain 'R' and resid 29 through 59
      removed outlier: 4.367A  pdb=" N   SER R  33 " --> pdb=" O   SER R  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 62
      No H-bonds generated for 'chain 'R' and resid 60 through 62'
    Processing helix  chain 'R' and resid 64 through 94
    Processing helix  chain 'R' and resid 98 through 102
      removed outlier: 4.320A  pdb=" N   PHE R 101 " --> pdb=" O   TRP R  98 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ASP R 102 " --> pdb=" O   ILE R  99 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 98 through 102'
    Processing helix  chain 'R' and resid 105 through 139
      Proline residue:  R 122  - end of helix
    Processing helix  chain 'R' and resid 139 through 146
    Processing helix  chain 'R' and resid 147 through 173
      removed outlier: 4.143A  pdb=" N   HIS R 151 " --> pdb=" O   ILE R 147 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   VAL R 152 " --> pdb=" O   THR R 148 " (cutoff:3.500A)
      Proline residue:  R 170  - end of helix
    Processing helix  chain 'R' and resid 195 through 229
      removed outlier: 3.906A  pdb=" N   ARG R 199 " --> pdb=" O   ASP R 195 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 244 through 275
      Proline residue:  R 264  - end of helix
    Processing helix  chain 'R' and resid 282 through 305
      removed outlier: 4.429A  pdb=" N   MET R 292 " --> pdb=" O   PHE R 288 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   TRP R 295 " --> pdb=" O   ARG R 291 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ASN R 296 " --> pdb=" O   MET R 292 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 313
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.899A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.414A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.537A  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: 6.993A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.620A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.071A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.108A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.528A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.081A  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: 6.674A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.791A  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: 6.515A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.542A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.337A  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 59 through 60
      removed outlier: 6.637A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 178 through 179

    397 hydrogen bonds defined for protein.
    1143 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.26

  Time building geometry restraints manager: 2.13 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: 1760
        1.33 -     1.45: 1435
        1.45 -     1.57: 3934
        1.57 -     1.69: 0
        1.69 -     1.81: 71
  Bond restraints: 7200
  Sorted by residual:
  bond pdb=" C02 7WT R 401 "
       pdb=" O01 7WT R 401 "
    ideal  model  delta    sigma   weight residual
    1.414  1.538 -0.124 2.00e-02 2.50e+03 3.85e+01
  bond pdb=" CA  ALA R 293 "
       pdb=" CB  ALA R 293 "
    ideal  model  delta    sigma   weight residual
    1.532  1.477  0.055 1.62e-02 3.81e+03 1.14e+01
  bond pdb=" C20 7WT R 401 "
       pdb=" C21 7WT R 401 "
    ideal  model  delta    sigma   weight residual
    1.497  1.556 -0.059 2.00e-02 2.50e+03 8.80e+00
  bond pdb=" CA  ALA R 289 "
       pdb=" CB  ALA R 289 "
    ideal  model  delta    sigma   weight residual
    1.530  1.482  0.049 1.69e-02 3.50e+03 8.30e+00
  bond pdb=" C22 7WT R 401 "
       pdb=" C23 7WT R 401 "
    ideal  model  delta    sigma   weight residual
    1.496  1.550 -0.054 2.00e-02 2.50e+03 7.20e+00
  ... (remaining 7195 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.74: 9729
        2.74 -     5.48: 61
        5.48 -     8.23: 4
        8.23 -    10.97: 3
       10.97 -    13.71: 1
  Bond angle restraints: 9798
  Sorted by residual:
  angle pdb=" N   LEU R 290 "
        pdb=" CA  LEU R 290 "
        pdb=" C   LEU R 290 "
      ideal   model   delta    sigma   weight residual
     111.36  102.64    8.72 1.09e+00 8.42e-01 6.40e+01
  angle pdb=" N   MET R 292 "
        pdb=" CA  MET R 292 "
        pdb=" C   MET R 292 "
      ideal   model   delta    sigma   weight residual
     113.38  107.19    6.19 1.23e+00 6.61e-01 2.53e+01
  angle pdb=" N   ALA R 293 "
        pdb=" CA  ALA R 293 "
        pdb=" C   ALA R 293 "
      ideal   model   delta    sigma   weight residual
     112.04  105.37    6.67 1.44e+00 4.82e-01 2.15e+01
  angle pdb=" C20 7WT R 401 "
        pdb=" C21 7WT R 401 "
        pdb=" C22 7WT R 401 "
      ideal   model   delta    sigma   weight residual
     128.03  114.32   13.71 3.00e+00 1.11e-01 2.09e+01
  angle pdb=" N   LEU R 287 "
        pdb=" CA  LEU R 287 "
        pdb=" C   LEU R 287 "
      ideal   model   delta    sigma   weight residual
     111.36  107.22    4.14 1.09e+00 8.42e-01 1.45e+01
  ... (remaining 9793 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.89: 3607
       15.89 -    31.77: 435
       31.77 -    47.66: 134
       47.66 -    63.55: 21
       63.55 -    79.44: 7
  Dihedral angle restraints: 4204
    sinusoidal: 1438
      harmonic: 2766
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -142.92   56.92     1      1.00e+01 1.00e-02 4.36e+01
  dihedral pdb=" CA  ARG R 100 "
           pdb=" C   ARG R 100 "
           pdb=" N   PHE R 101 "
           pdb=" CA  PHE R 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.29   24.71     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  CYS N  99 "
           pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   13.87   65.13     1      2.00e+01 2.50e-03 1.39e+01
  ... (remaining 4201 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1079
       0.078 -    0.156: 86
       0.156 -    0.234: 2
       0.234 -    0.312: 1
       0.312 -    0.391: 2
  Chirality restraints: 1170
  Sorted by residual:
  chirality pdb=" C03 7WT R 401 "
            pdb=" C02 7WT R 401 "
            pdb=" C04 7WT R 401 "
            pdb=" C20 7WT R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.92    0.39 2.00e-01 2.50e+01 3.81e+00
  chirality pdb=" C04 7WT R 401 "
            pdb=" C03 7WT R 401 "
            pdb=" C05 7WT R 401 "
            pdb=" C08 7WT R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.63    2.97   -0.34 2.00e-01 2.50e+01 2.97e+00
  chirality pdb=" CA  LEU R 290 "
            pdb=" N   LEU R 290 "
            pdb=" C   LEU R 290 "
            pdb=" CB  LEU R 290 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.73e+00
  ... (remaining 1167 not shown)

  Planarity restraints: 1222
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  87 "    0.010 2.00e-02 2.50e+03   1.91e-02 3.64e+00
        pdb=" C   THR B  87 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   THR B  87 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ASN B  88 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "   -0.028 5.00e-02 4.00e+02   4.20e-02 2.82e+00
        pdb=" N   PRO G  49 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO B 236 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1219 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1627
        2.78 -     3.31: 6367
        3.31 -     3.84: 11555
        3.84 -     4.37: 12921
        4.37 -     4.90: 23796
  Nonbonded interactions: 56266
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   SER N 112 "
            pdb=" NH2 ARG N 118 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   MET B 188 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OD2 ASP A  33 "
            pdb=" NZ  LYS B  78 "
     model   vdw
     2.271 3.120
  ... (remaining 56261 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:             0.720
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.440
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
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   0.124   7200  Z= 0.253
  Angle     :  0.586  13.711   9798  Z= 0.324
  Chirality :  0.045   0.391   1170
  Planarity :  0.004   0.064   1222
  Dihedral  : 15.453  79.436   2401
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 18.83 %
    Favored  : 80.88 %
  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:  1.39 (0.28), residues: 930
  helix:  3.05 (0.27), residues: 354
  sheet:  0.50 (0.36), residues: 202
  loop : -1.01 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.015   0.001   PHE R 101 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.008   0.000   ARG R  57 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
REVERT: R  217 LEU cc_start: 0.8668 (tp) cc_final: 0.8225 (tp)
REVERT: R  291 ARG cc_start: 0.8164 (ptp-170) cc_final: 0.6998 (ptm160)
  outliers start: 2
  outliers final: 1
  residues processed: 119
  average time/residue: 0.2236
  time to fit residues: 34.7988
Evaluate side-chains
  115 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  287 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 28 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 392 ASN
R 189 ASN
R 243 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.133201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.113928 restraints weight = 9579.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.46
r_work: 0.3226 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.0661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7200  Z= 0.220
  Angle     :  0.480   6.140   9798  Z= 0.264
  Chirality :  0.041   0.132   1170
  Planarity :  0.003   0.043   1222
  Dihedral  :  5.157  55.267   1048
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 17.66 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.28), residues: 930
  helix:  2.90 (0.27), residues: 364
  sheet:  0.46 (0.36), residues: 203
  loop : -1.06 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.017   0.001   PHE B 199 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.005   0.000   ARG R 183 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
REVERT: A  378 ASP cc_start: 0.8094 (m-30) cc_final: 0.7689 (m-30)
REVERT: B  237 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8523 (p0)
REVERT: B  336 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8647 (tt)
REVERT: R  115 MET cc_start: 0.8697 (mmm) cc_final: 0.8270 (tpt)
REVERT: R  246 GLU cc_start: 0.7888 (mp0) cc_final: 0.7271 (tp30)
REVERT: R  291 ARG cc_start: 0.8118 (ptp-170) cc_final: 0.6778 (ptm160)
  outliers start: 19
  outliers final: 10
  residues processed: 134
  average time/residue: 0.2071
  time to fit residues: 36.4976
Evaluate side-chains
  127 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  287 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 7 optimal weight:    0.3980
   chunk 22 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 90 optimal weight:    0.5980
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.134907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.114949 restraints weight = 9608.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 1.52
r_work: 0.3045 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.0840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7200  Z= 0.175
  Angle     :  0.449   5.617   9798  Z= 0.248
  Chirality :  0.040   0.134   1170
  Planarity :  0.003   0.042   1222
  Dihedral  :  4.869  52.451   1048
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.66 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.10 %
    Favored  : 79.12 %
  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:  1.45 (0.28), residues: 930
  helix:  3.10 (0.27), residues: 358
  sheet:  0.49 (0.36), residues: 202
  loop : -1.00 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.015   0.001   PHE R 101 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.004   0.000   ARG R  57 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
REVERT: B  237 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8575 (p0)
REVERT: B  336 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8463 (tt)
REVERT: R   56 GLN cc_start: 0.7660 (mm110) cc_final: 0.7283 (mm-40)
REVERT: R   59 ARG cc_start: 0.7968 (tmm-80) cc_final: 0.7410 (ttp-170)
REVERT: R   61 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8331 (mttp)
REVERT: R  115 MET cc_start: 0.8591 (mmm) cc_final: 0.8085 (tpt)
REVERT: R  246 GLU cc_start: 0.7856 (mp0) cc_final: 0.6967 (tp30)
  outliers start: 19
  outliers final: 8
  residues processed: 131
  average time/residue: 0.2043
  time to fit residues: 35.4004
Evaluate side-chains
  123 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  208 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 16 optimal weight:    0.1980
   chunk 57 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0870
   chunk 82 optimal weight:    0.1980
   chunk 14 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 91 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
R 180 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.136743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.116849 restraints weight = 9641.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 1.51
r_work: 0.3259 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7200  Z= 0.142
  Angle     :  0.427   5.415   9798  Z= 0.235
  Chirality :  0.040   0.134   1170
  Planarity :  0.003   0.038   1222
  Dihedral  :  4.286  29.000   1046
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.44 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 17.81 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.54 (0.28), residues: 930
  helix:  3.21 (0.26), residues: 359
  sheet:  0.53 (0.36), residues: 209
  loop : -1.03 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.000   HIS A 357 
 PHE   0.016   0.001   PHE R 101 
 TYR   0.009   0.001   TYR N  95 
 ARG   0.005   0.000   ARG R  57 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
REVERT: A  378 ASP cc_start: 0.8110 (m-30) cc_final: 0.7646 (m-30)
REVERT: B  237 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8303 (p0)
REVERT: B  246 ASP cc_start: 0.8509 (m-30) cc_final: 0.8203 (m-30)
REVERT: B  336 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8460 (tt)
REVERT: R   56 GLN cc_start: 0.7686 (mm110) cc_final: 0.7234 (mm-40)
REVERT: R   59 ARG cc_start: 0.7929 (tmm-80) cc_final: 0.7495 (ttp-170)
REVERT: R  115 MET cc_start: 0.8741 (mmm) cc_final: 0.8288 (tpt)
REVERT: R  246 GLU cc_start: 0.7896 (mp0) cc_final: 0.7196 (tp30)
  outliers start: 18
  outliers final: 12
  residues processed: 136
  average time/residue: 0.2158
  time to fit residues: 38.2621
Evaluate side-chains
  130 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue  133 ARG
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  208 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0570
   chunk 54 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 84 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
R 189 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.135570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.115731 restraints weight = 9553.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.50
r_work: 0.3248 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7200  Z= 0.176
  Angle     :  0.448   5.377   9798  Z= 0.244
  Chirality :  0.040   0.136   1170
  Planarity :  0.003   0.041   1222
  Dihedral  :  4.275  29.202   1046
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.44 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 19.12 %
    Favored  : 78.39 %
  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:  1.50 (0.28), residues: 930
  helix:  3.22 (0.26), residues: 358
  sheet:  0.46 (0.35), residues: 210
  loop : -1.05 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.016   0.001   PHE R 101 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.005   0.000   ARG R 229 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
REVERT: B  237 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8342 (p0)
REVERT: B  246 ASP cc_start: 0.8519 (m-30) cc_final: 0.8210 (m-30)
REVERT: B  336 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8488 (tt)
REVERT: R   56 GLN cc_start: 0.7616 (mm110) cc_final: 0.7195 (mm-40)
REVERT: R   59 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7489 (ttp-170)
REVERT: R  115 MET cc_start: 0.8781 (mmm) cc_final: 0.8319 (tpt)
REVERT: R  246 GLU cc_start: 0.7855 (mp0) cc_final: 0.7166 (tp30)
  outliers start: 17
  outliers final: 13
  residues processed: 123
  average time/residue: 0.2121
  time to fit residues: 34.4472
Evaluate side-chains
  127 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue  133 ARG
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  292 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 28 optimal weight:    0.4980
   chunk 30 optimal weight:    0.6980
   chunk 91 optimal weight:    0.8980
   chunk 84 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
R 189 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.134568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.114622 restraints weight = 9679.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 1.52
r_work: 0.3232 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7200  Z= 0.197
  Angle     :  0.454   5.337   9798  Z= 0.248
  Chirality :  0.041   0.146   1170
  Planarity :  0.003   0.043   1222
  Dihedral  :  4.248  28.586   1046
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.66 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 19.27 %
    Favored  : 77.81 %
  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:  1.50 (0.28), residues: 930
  helix:  3.27 (0.26), residues: 358
  sheet:  0.43 (0.35), residues: 210
  loop : -1.09 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.016   0.001   PHE R 101 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.006   0.000   ARG R  57 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
REVERT: A  378 ASP cc_start: 0.8142 (m-30) cc_final: 0.7719 (m-30)
REVERT: B  237 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8416 (p0)
REVERT: B  246 ASP cc_start: 0.8555 (m-30) cc_final: 0.8242 (m-30)
REVERT: B  336 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8508 (tt)
REVERT: R   56 GLN cc_start: 0.7675 (mm110) cc_final: 0.7281 (mm-40)
REVERT: R   59 ARG cc_start: 0.7984 (ttm-80) cc_final: 0.7519 (ttp-170)
REVERT: R  246 GLU cc_start: 0.7868 (mp0) cc_final: 0.7182 (tp30)
  outliers start: 20
  outliers final: 15
  residues processed: 125
  average time/residue: 0.2048
  time to fit residues: 33.8095
Evaluate side-chains
  128 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue  133 ARG
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  208 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.133847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.113865 restraints weight = 9634.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.52
r_work: 0.3221 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.1240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7200  Z= 0.214
  Angle     :  0.469   5.287   9798  Z= 0.256
  Chirality :  0.041   0.148   1170
  Planarity :  0.003   0.045   1222
  Dihedral  :  4.239  27.640   1046
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.23 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 19.27 %
    Favored  : 77.52 %
  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:  1.46 (0.28), residues: 930
  helix:  3.24 (0.26), residues: 358
  sheet:  0.38 (0.35), residues: 210
  loop : -1.10 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.016   0.001   PHE R 101 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.007   0.000   ARG R  57 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
REVERT: B  237 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8486 (p0)
REVERT: B  246 ASP cc_start: 0.8550 (m-30) cc_final: 0.8234 (m-30)
REVERT: B  336 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8546 (tt)
REVERT: R   56 GLN cc_start: 0.7709 (mm110) cc_final: 0.7317 (mm-40)
REVERT: R   59 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7519 (ttp-170)
REVERT: R  200 PHE cc_start: 0.8466 (t80) cc_final: 0.8030 (t80)
REVERT: R  246 GLU cc_start: 0.7863 (mp0) cc_final: 0.7175 (tp30)
  outliers start: 22
  outliers final: 15
  residues processed: 128
  average time/residue: 0.2050
  time to fit residues: 35.2705
Evaluate side-chains
  128 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue  133 ARG
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  287 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0980
   chunk 85 optimal weight:    4.9990
   chunk 47 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 189 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.135269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.115464 restraints weight = 9584.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 1.50
r_work: 0.3242 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7200  Z= 0.170
  Angle     :  0.457   5.209   9798  Z= 0.248
  Chirality :  0.041   0.148   1170
  Planarity :  0.003   0.043   1222
  Dihedral  :  4.108  24.414   1046
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.66 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 19.42 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.28), residues: 930
  helix:  3.26 (0.26), residues: 358
  sheet:  0.43 (0.35), residues: 210
  loop : -1.11 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.017   0.001   PHE R 101 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.008   0.000   ARG R  57 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 116
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ARG cc_start: 0.7284 (mmm-85) cc_final: 0.6880 (tpp80)
REVERT: B  237 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8416 (p0)
REVERT: B  246 ASP cc_start: 0.8547 (m-30) cc_final: 0.8255 (m-30)
REVERT: B  336 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8586 (tt)
REVERT: R   56 GLN cc_start: 0.7679 (mm110) cc_final: 0.7287 (mm-40)
REVERT: R   59 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7474 (ttp-170)
REVERT: R  200 PHE cc_start: 0.8377 (t80) cc_final: 0.7962 (t80)
REVERT: R  217 LEU cc_start: 0.8580 (tp) cc_final: 0.8161 (tp)
REVERT: R  246 GLU cc_start: 0.7788 (mp0) cc_final: 0.7175 (tp30)
  outliers start: 22
  outliers final: 18
  residues processed: 126
  average time/residue: 0.2484
  time to fit residues: 41.3970
Evaluate side-chains
  134 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 1.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain N residue   53 GLN
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue  133 ARG
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  287 LEU
Chi-restraints excluded: chain R residue  292 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
G  44 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.134356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.114456 restraints weight = 9781.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3093 rms_B_bonded: 1.51
r_work: 0.3006 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.1294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7200  Z= 0.202
  Angle     :  0.474   6.168   9798  Z= 0.255
  Chirality :  0.041   0.147   1170
  Planarity :  0.003   0.045   1222
  Dihedral  :  4.132  23.829   1046
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.55 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.00 %
    Favored  : 77.08 %
  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:  1.48 (0.28), residues: 930
  helix:  3.26 (0.26), residues: 358
  sheet:  0.41 (0.35), residues: 210
  loop : -1.11 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.008   0.000   ARG R  57 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ARG cc_start: 0.7491 (mmm-85) cc_final: 0.7064 (tpp80)
REVERT: B  237 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8495 (p0)
REVERT: B  246 ASP cc_start: 0.8623 (m-30) cc_final: 0.8260 (m-30)
REVERT: B  336 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8420 (tt)
REVERT: R   56 GLN cc_start: 0.7545 (mm110) cc_final: 0.7179 (mm-40)
REVERT: R   59 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7397 (ttp-170)
REVERT: R  200 PHE cc_start: 0.8308 (t80) cc_final: 0.7922 (t80)
REVERT: R  217 LEU cc_start: 0.8587 (tp) cc_final: 0.8164 (tp)
REVERT: R  246 GLU cc_start: 0.7758 (mp0) cc_final: 0.6934 (tp30)
  outliers start: 20
  outliers final: 17
  residues processed: 125
  average time/residue: 0.2041
  time to fit residues: 33.6549
Evaluate side-chains
  131 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain N residue   53 GLN
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue  133 ARG
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  287 LEU
Chi-restraints excluded: chain R residue  292 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 7 optimal weight:    0.3980
   chunk 83 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 19 optimal weight:    0.3980
   chunk 56 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.134879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.114907 restraints weight = 9839.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 1.53
r_work: 0.3238 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7200  Z= 0.179
  Angle     :  0.463   6.223   9798  Z= 0.249
  Chirality :  0.041   0.145   1170
  Planarity :  0.003   0.044   1222
  Dihedral  :  4.072  24.014   1046
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.66 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 19.56 %
    Favored  : 77.52 %
  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:  1.49 (0.28), residues: 930
  helix:  3.27 (0.26), residues: 358
  sheet:  0.44 (0.35), residues: 210
  loop : -1.12 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.016   0.001   PHE R  78 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.008   0.000   ARG R  57 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ARG cc_start: 0.7268 (mmm-85) cc_final: 0.6873 (tpp80)
REVERT: A  378 ASP cc_start: 0.8133 (m-30) cc_final: 0.7687 (m-30)
REVERT: B  237 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8386 (p0)
REVERT: B  246 ASP cc_start: 0.8584 (m-30) cc_final: 0.8281 (m-30)
REVERT: B  336 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8502 (tt)
REVERT: R   56 GLN cc_start: 0.7597 (mm110) cc_final: 0.7205 (mm-40)
REVERT: R   59 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7519 (ttp-170)
REVERT: R  200 PHE cc_start: 0.8397 (t80) cc_final: 0.7998 (t80)
REVERT: R  217 LEU cc_start: 0.8584 (tp) cc_final: 0.8161 (tp)
REVERT: R  246 GLU cc_start: 0.7766 (mp0) cc_final: 0.7155 (tp30)
  outliers start: 20
  outliers final: 18
  residues processed: 124
  average time/residue: 0.2799
  time to fit residues: 45.6401
Evaluate side-chains
  133 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain N residue   53 GLN
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue  133 ARG
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  287 LEU
Chi-restraints excluded: chain R residue  292 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0570
   chunk 77 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.6900

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

Flipped N/Q/H residues before XYZ refinement:
A 271 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.134711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.114869 restraints weight = 9650.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 1.50
r_work: 0.3236 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7200  Z= 0.186
  Angle     :  0.468   6.747   9798  Z= 0.251
  Chirality :  0.041   0.146   1170
  Planarity :  0.003   0.044   1222
  Dihedral  :  4.061  23.281   1046
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.44 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 19.56 %
    Favored  : 77.52 %
  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:  1.51 (0.28), residues: 930
  helix:  3.30 (0.26), residues: 358
  sheet:  0.43 (0.35), residues: 210
  loop : -1.11 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.009   0.000   ARG R  57 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3825.97 seconds
wall clock time: 68 minutes 32.10 seconds (4112.10 seconds total)