Starting phenix.real_space_refine
on Tue Mar 11 15:22:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6u1n_20612/03_2025/6u1n_20612.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6u1n_20612/03_2025/6u1n_20612.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6u1n_20612/03_2025/6u1n_20612.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6u1n_20612/03_2025/6u1n_20612.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6u1n_20612/03_2025/6u1n_20612.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6u1n_20612/03_2025/6u1n_20612.cif"
  }
  resolution = 4.0
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 102 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      15      5.16       5
     Cl      1      4.86       5
     C    3739      2.51       5
     N    1012      2.21       5
     O    1090      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 5863
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 1660
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 1660
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 169}
          Link IDs: {'PTRANS': 10, 'TRANS': 267}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 586
          Unresolved non-hydrogen angles: 767
          Unresolved non-hydrogen dihedrals: 475
          Unresolved non-hydrogen chiralities: 86
          Planarities with less than four sites: {'GLN:plan1': 3, 'TPO:plan-1': 2, 'ASP:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 13, 'GLU:plan': 5, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 264
    Chain: "C"
      Number of atoms: 2547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 359, 2547
          Classifications: {'peptide': 359}
          Incomplete info: {'truncation_to_alanine': 83}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 331}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 308
          Unresolved non-hydrogen angles: 379
          Unresolved non-hydrogen dihedrals: 244
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 204
    Chain: "H"
      Number of atoms: 846
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 846
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 2, 'TRANS': 116}
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 90
          Unresolved non-hydrogen dihedrals: 58
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 52
    Chain: "L"
      Number of atoms: 781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 781
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "R"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'2CU': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.14, per 1000 atoms: 0.88
  Number of scatterers: 5863
  At special positions: 0
  Unit cell: (118.72, 116.6, 90.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      15     16.00
     P       6     15.00
     O    1090      8.00
     N    1012      7.00
     C    3739      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 176 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 413 " - pdb=" SG  CYS R 416 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.04

  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: 1.80
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1632

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 11 sheets defined
      32.3% alpha, 27.1% 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 20 through 48
      removed outlier: 4.113A  pdb=" N   LEU R  28 " --> pdb=" O   VAL R  24 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLY R  31 " --> pdb=" O   VAL R  27 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LEU R  35 " --> pdb=" O   GLY R  31 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL R  36 " --> pdb=" O   SER R  32 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   THR R  37 " --> pdb=" O   LEU R  33 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   ILE R  38 " --> pdb=" O   SER R  34 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLY R  40 " --> pdb=" O   VAL R  36 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ILE R  42 " --> pdb=" O   ILE R  38 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU R  43 " --> pdb=" O   ILE R  39 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ILE R  48 " --> pdb=" O   VAL R  44 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 56 through 75
      removed outlier: 4.555A  pdb=" N   LEU R  62 " --> pdb=" O   ASN R  58 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ALA R  66 " --> pdb=" O   LEU R  62 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   ILE R  71 " --> pdb=" O   CYS R  67 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ILE R  72 " --> pdb=" O   ALA R  68 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   GLY R  73 " --> pdb=" O   ASP R  69 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 75 through 87
      removed outlier: 3.859A  pdb=" N   THR R  81 " --> pdb=" O   MET R  77 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LEU R  82 " --> pdb=" O   ASN R  78 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 92 through 117
      removed outlier: 4.083A  pdb=" N   LEU R  98 " --> pdb=" O   VAL R  94 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LEU R 100 " --> pdb=" O   CYS R  96 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ALA R 101 " --> pdb=" O   ASP R  97 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ILE R 116 " --> pdb=" O   MET R 112 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 119 through 127
      removed outlier: 3.766A  pdb=" N   VAL R 125 " --> pdb=" O   ARG R 121 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 130 through 135
    Processing helix  chain 'R' and resid 136 through 167
      removed outlier: 4.142A  pdb=" N   MET R 142 " --> pdb=" O   LYS R 138 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   ALA R 147 " --> pdb=" O   MET R 143 " (cutoff:3.500A)
      Proline residue:  R 157  - end of helix
      removed outlier: 4.501A  pdb=" N   GLN R 163 " --> pdb=" O   ILE R 159 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   PHE R 164 " --> pdb=" O   LEU R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 183 through 213
      removed outlier: 3.533A  pdb=" N   THR R 187 " --> pdb=" O   ASN R 183 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   GLY R 189 " --> pdb=" O   ALA R 185 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ALA R 191 " --> pdb=" O   THR R 187 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   ILE R 192 " --> pdb=" O   PHE R 188 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   LEU R 197 " --> pdb=" O   ALA R 193 " (cutoff:3.500A)
      Proline residue:  R 198  - end of helix
      removed outlier: 3.756A  pdb=" N   ALA R 212 " --> pdb=" O   HIS R 208 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   SER R 213 " --> pdb=" O   ILE R 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 383 through 414
      removed outlier: 4.234A  pdb=" N   LEU R 390 " --> pdb=" O   THR R 386 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ALA R 391 " --> pdb=" O   ARG R 387 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   TRP R 400 " --> pdb=" O   PHE R 396 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA R 401 " --> pdb=" O   ILE R 397 " (cutoff:3.500A)
      Proline residue:  R 402  - end of helix
      removed outlier: 4.086A  pdb=" N   LEU R 408 " --> pdb=" O   ASN R 404 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   ILE R 409 " --> pdb=" O   VAL R 405 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   THR R 411 " --> pdb=" O   VAL R 407 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 415 through 417
      No H-bonds generated for 'chain 'R' and resid 415 through 417'
    Processing helix  chain 'R' and resid 418 through 431
      removed outlier: 3.734A  pdb=" N   THR R 423 " --> pdb=" O   ASN R 419 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ILE R 424 " --> pdb=" O   THR R 420 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   TYR R 426 " --> pdb=" O   TRP R 422 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 431 through 441
      Proline residue:  R 437  - end of helix
      removed outlier: 3.747A  pdb=" N   TYR R 440 " --> pdb=" O   ASN R 436 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ALA R 441 " --> pdb=" O   PRO R 437 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 444 through 452
    Processing helix  chain 'C' and resid 98 through 108
    Processing helix  chain 'C' and resid 159 through 163
    Processing helix  chain 'C' and resid 278 through 282
      removed outlier: 3.927A  pdb=" N   ARG C 282 " --> pdb=" O   ALA C 279 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 31 through 35
    Processing helix  chain 'H' and resid 56 through 59
    Processing helix  chain 'H' and resid 65 through 68
      removed outlier: 3.593A  pdb=" N   LYS H  68 " --> pdb=" O   ASP H  65 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 65 through 68'
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 3.692A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
    Processing sheet with id=AA1, first strand: chain 'R' and resid 492 through 495
    Processing sheet with id=AA2, first strand: chain 'C' and resid 29 through 30
    Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 87
      removed outlier: 6.763A  pdb=" N   VAL C  59 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   VAL C  81 " --> pdb=" O   LEU C  57 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   LEU C  57 " --> pdb=" O   VAL C  81 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   ASN C  83 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   VAL C  55 " --> pdb=" O   ASN C  83 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   GLN C  85 " --> pdb=" O   VAL C  53 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   VAL C  53 " --> pdb=" O   GLN C  85 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   TYR C 144 " --> pdb=" O   ILE C 168 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 128 through 129
    Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 188
    Processing sheet with id=AA6, first strand: chain 'C' and resid 207 through 209
      removed outlier: 4.065A  pdb=" N   TYR C 321 " --> pdb=" O   PHE C 349 " (cutoff:3.500A)
      removed outlier: 7.848A  pdb=" N   LEU C 351 " --> pdb=" O   VAL C 319 " (cutoff:3.500A)
      removed outlier: 9.554A  pdb=" N   VAL C 319 " --> pdb=" O   LEU C 351 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   ILE C 318 " --> pdb=" O   ALA C 239 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   ALA C 239 " --> pdb=" O   ILE C 318 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   SER C 320 " --> pdb=" O   GLN C 237 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   GLN C 237 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LYS C 322 " --> pdb=" O   VAL C 235 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   VAL C 235 " --> pdb=" O   LYS C 322 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   LYS C 324 " --> pdb=" O   ILE C 233 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   ILE C 233 " --> pdb=" O   LYS C 324 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   LYS C 326 " --> pdb=" O   ILE C 231 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   ILE C 231 " --> pdb=" O   LYS C 326 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   VAL C 328 " --> pdb=" O   LYS C 229 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   THR C 227 " --> pdb=" O   SER C 330 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   GLN C 237 " --> pdb=" O   PRO C 252 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   ALA C 239 " --> pdb=" O   LYS C 250 " (cutoff:3.500A)
      removed outlier: 5.528A  pdb=" N   LYS C 250 " --> pdb=" O   ALA C 239 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   ILE C 241 " --> pdb=" O   GLN C 248 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   GLN C 248 " --> pdb=" O   ILE C 241 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 7 through 10
    Processing sheet with id=AA8, first strand: chain 'H' and resid 14 through 15
      removed outlier: 6.784A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 14 through 15
      removed outlier: 3.816A  pdb=" N   TYR H 112 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 8
    Processing sheet with id=AB2, first strand: chain 'L' and resid 12 through 14
      removed outlier: 6.497A  pdb=" N   LEU L  12 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)

    289 hydrogen bonds defined for protein.
    774 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: 2.01

  Time building geometry restraints manager: 2.05 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1004
        1.32 -     1.46: 2108
        1.46 -     1.59: 2846
        1.59 -     1.73: 19
        1.73 -     1.86: 21
  Bond restraints: 5998
  Sorted by residual:
  bond pdb=" C22 2CU R 601 "
       pdb=" S21 2CU R 601 "
    ideal  model  delta    sigma   weight residual
    1.721  1.862 -0.141 2.00e-02 2.50e+03 4.95e+01
  bond pdb=" C03 2CU R 601 "
       pdb=" N02 2CU R 601 "
    ideal  model  delta    sigma   weight residual
    1.449  1.316  0.133 2.00e-02 2.50e+03 4.45e+01
  bond pdb=" C07 2CU R 601 "
       pdb=" N02 2CU R 601 "
    ideal  model  delta    sigma   weight residual
    1.448  1.318  0.130 2.00e-02 2.50e+03 4.25e+01
  bond pdb=" C08 2CU R 601 "
       pdb=" N05 2CU R 601 "
    ideal  model  delta    sigma   weight residual
    1.346  1.476 -0.130 2.00e-02 2.50e+03 4.20e+01
  bond pdb=" C01 2CU R 601 "
       pdb=" N02 2CU R 601 "
    ideal  model  delta    sigma   weight residual
    1.445  1.323  0.122 2.00e-02 2.50e+03 3.74e+01
  ... (remaining 5993 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.64: 8151
        2.64 -     5.28: 96
        5.28 -     7.92: 14
        7.92 -    10.55: 2
       10.55 -    13.19: 3
  Bond angle restraints: 8266
  Sorted by residual:
  angle pdb=" OG1 TPO R 490 "
        pdb=" P   TPO R 490 "
        pdb=" O1P TPO R 490 "
      ideal   model   delta    sigma   weight residual
     100.43  113.62  -13.19 3.00e+00 1.11e-01 1.93e+01
  angle pdb=" CB  TPO R 491 "
        pdb=" OG1 TPO R 491 "
        pdb=" P   TPO R 491 "
      ideal   model   delta    sigma   weight residual
     119.31  106.42   12.89 3.00e+00 1.11e-01 1.85e+01
  angle pdb=" CB  SEP R 493 "
        pdb=" OG  SEP R 493 "
        pdb=" P   SEP R 493 "
      ideal   model   delta    sigma   weight residual
     110.00  120.57  -10.57 3.00e+00 1.11e-01 1.24e+01
  angle pdb=" C17 2CU R 601 "
        pdb=" C18 2CU R 601 "
        pdb=" C20 2CU R 601 "
      ideal   model   delta    sigma   weight residual
     111.70  122.11  -10.41 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" CA  HIS C 362 "
        pdb=" C   HIS C 362 "
        pdb=" O   HIS C 362 "
      ideal   model   delta    sigma   weight residual
     122.14  118.31    3.83 1.24e+00 6.50e-01 9.53e+00
  ... (remaining 8261 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.11: 3441
       29.11 -    58.21: 59
       58.21 -    87.32: 5
       87.32 -   116.42: 0
      116.42 -   145.53: 1
  Dihedral angle restraints: 3506
    sinusoidal: 978
      harmonic: 2528
  Sorted by residual:
  dihedral pdb=" CB  CYS R  96 "
           pdb=" SG  CYS R  96 "
           pdb=" SG  CYS R 176 "
           pdb=" CB  CYS R 176 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -154.52   68.52     1      1.00e+01 1.00e-02 6.08e+01
  dihedral pdb=" CB  CYS R 413 "
           pdb=" SG  CYS R 413 "
           pdb=" SG  CYS R 416 "
           pdb=" CB  CYS R 416 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  150.39  -57.39     1      1.00e+01 1.00e-02 4.43e+01
  dihedral pdb=" C29 2CU R 601 "
           pdb=" C27 2CU R 601 "
           pdb=" C28 2CU R 601 "
           pdb=" N26 2CU R 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     250.71  105.18  145.53     1      3.00e+01 1.11e-03 1.95e+01
  ... (remaining 3503 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 806
       0.055 -    0.111: 167
       0.111 -    0.166: 16
       0.166 -    0.221: 0
       0.221 -    0.276: 2
  Chirality restraints: 991
  Sorted by residual:
  chirality pdb=" C27 2CU R 601 "
            pdb=" C28 2CU R 601 "
            pdb=" C29 2CU R 601 "
            pdb=" N26 2CU R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.31    2.59   -0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" CA  ILE L  22 "
            pdb=" N   ILE L  22 "
            pdb=" C   ILE L  22 "
            pdb=" CB  ILE L  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CA  TYR L  92 "
            pdb=" N   TYR L  92 "
            pdb=" C   TYR L  92 "
            pdb=" CB  TYR L  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.08e-01
  ... (remaining 988 not shown)

  Planarity restraints: 1056
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H 106 "    0.018 2.00e-02 2.50e+03   1.55e-02 6.02e+00
        pdb=" CG  TRP H 106 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP H 106 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP H 106 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP H 106 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP H 106 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP H 106 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H 106 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H 106 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP H 106 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 197 "   -0.028 5.00e-02 4.00e+02   4.20e-02 2.83e+00
        pdb=" N   PRO R 198 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO R 198 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO R 198 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER L  66 "    0.007 2.00e-02 2.50e+03   1.33e-02 1.76e+00
        pdb=" C   SER L  66 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   SER L  66 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ARG L  67 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1053 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 697
        2.74 -     3.28: 6435
        3.28 -     3.82: 9358
        3.82 -     4.36: 10725
        4.36 -     4.90: 17854
  Nonbonded interactions: 45069
  Sorted by model distance:
  nonbonded pdb=" O   LYS C 195 "
            pdb=" OG1 THR C 224 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" NH1 ARG L  19 "
            pdb=" OG1 THR L  75 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   ASN C 222 "
            pdb=" N   SER C 265 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" OH  TYR H  63 "
            pdb=" N   ILE H  73 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" OG1 THR C 183 "
            pdb=" O   ALA C 201 "
     model   vdw
     2.255 3.040
  ... (remaining 45064 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 group one per residue
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:             0.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.280
  Find NCS groups from input model:        0.080
  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:             0.010
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
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      :  0.008   0.141   5998  Z= 0.552
  Angle     :  0.808  13.192   8266  Z= 0.429
  Chirality :  0.044   0.276    991
  Planarity :  0.004   0.042   1056
  Dihedral  : 12.150 145.527   1862
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 17.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.13 %
    Favored  : 90.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -4.67 (0.23), residues: 843
  helix: -3.58 (0.23), residues: 186
  sheet: -2.48 (0.29), residues: 263
  loop : -3.24 (0.26), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP H 106 
 HIS   0.003   0.001   HIS C 353 
 PHE   0.020   0.002   PHE H 105 
 TYR   0.012   0.001   TYR L  50 
 ARG   0.006   0.001   ARG L  19 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.9037 (m-80) cc_final: 0.8461 (m-80)
REVERT: H   16 GLN cc_start: 0.8429 (mm110) cc_final: 0.8126 (mm-40)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.1708
  time to fit residues: 18.4216
Evaluate side-chains
  61 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.5980
   chunk 25 optimal weight:    7.9990
   chunk 39 optimal weight:    0.5980
   chunk 48 optimal weight:    8.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
R  58 ASN
** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 162 ASN
C 172 GLN
C 198 HIS
H  16 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  91 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.065336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.046677 restraints weight = 31823.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.048106 restraints weight = 17046.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.049017 restraints weight = 11644.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5998  Z= 0.182
  Angle     :  0.580   6.494   8266  Z= 0.298
  Chirality :  0.044   0.169    991
  Planarity :  0.004   0.031   1056
  Dihedral  :  8.393 141.090    942
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.00 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.96 (0.26), residues: 843
  helix: -1.40 (0.32), residues: 217
  sheet: -1.81 (0.29), residues: 267
  loop : -2.31 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP R 207 
 HIS   0.002   0.001   HIS C  30 
 PHE   0.018   0.001   PHE H  30 
 TYR   0.016   0.001   TYR R 131 
 ARG   0.005   0.001   ARG L  67 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8833 (m-80) cc_final: 0.8235 (m-80)
REVERT: R  397 ILE cc_start: 0.9495 (mt) cc_final: 0.9270 (pt)
REVERT: C  144 TYR cc_start: 0.8181 (m-80) cc_final: 0.7978 (m-80)
REVERT: H   16 GLN cc_start: 0.8306 (mm-40) cc_final: 0.8064 (mm-40)
REVERT: L   22 ILE cc_start: 0.9430 (mm) cc_final: 0.9208 (mt)
  outliers start: 12
  outliers final: 6
  residues processed: 83
  average time/residue: 0.1526
  time to fit residues: 17.6616
Evaluate side-chains
  70 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  207 ILE
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   76 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 5 optimal weight:    8.9990
   chunk 3 optimal weight:   20.0000
   chunk 72 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0670
   chunk 66 optimal weight:    0.9980
   chunk 33 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.2122

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

Flipped N/Q/H residues before XYZ refinement:
C 130 GLN
** L  90 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 = 0.3493 r_free = 0.3493 target = 0.065717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.046900 restraints weight = 31686.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.048359 restraints weight = 16708.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.049298 restraints weight = 11329.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5998  Z= 0.175
  Angle     :  0.561   8.552   8266  Z= 0.282
  Chirality :  0.043   0.172    991
  Planarity :  0.003   0.028   1056
  Dihedral  :  8.146 140.579    942
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 15.22 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.96 (0.28), residues: 843
  helix: -0.32 (0.35), residues: 216
  sheet: -1.39 (0.31), residues: 261
  loop : -1.72 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 155 
 HIS   0.002   0.001   HIS C 353 
 PHE   0.015   0.001   PHE H 105 
 TYR   0.013   0.001   TYR R 104 
 ARG   0.004   0.001   ARG R 121 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8778 (m-80) cc_final: 0.8204 (m-80)
REVERT: R  400 TRP cc_start: 0.7449 (m100) cc_final: 0.7031 (m100)
REVERT: C  144 TYR cc_start: 0.8505 (m-80) cc_final: 0.8209 (m-80)
REVERT: H   16 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8043 (mm-40)
REVERT: L   22 ILE cc_start: 0.9442 (mm) cc_final: 0.9240 (mt)
  outliers start: 16
  outliers final: 9
  residues processed: 83
  average time/residue: 0.1586
  time to fit residues: 18.4668
Evaluate side-chains
  74 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  207 ILE
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  317 ILE
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   76 ILE
Chi-restraints excluded: chain L residue   95 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 14 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9980
   chunk 4 optimal weight:   20.0000
   chunk 7 optimal weight:   20.0000
   chunk 82 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 43 optimal weight:    0.7980
   chunk 52 optimal weight:    9.9990
   overall best weight:    3.7586

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

Flipped N/Q/H residues before XYZ refinement:
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.063252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.044594 restraints weight = 32775.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.045924 restraints weight = 17990.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.046753 restraints weight = 12401.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   5998  Z= 0.395
  Angle     :  0.647   7.529   8266  Z= 0.332
  Chirality :  0.044   0.161    991
  Planarity :  0.004   0.028   1056
  Dihedral  :  8.397 140.574    942
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 17.61 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.75 (0.29), residues: 843
  helix: -0.00 (0.36), residues: 218
  sheet: -1.25 (0.32), residues: 252
  loop : -1.72 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP H 106 
 HIS   0.004   0.001   HIS C 353 
 PHE   0.021   0.002   PHE H 105 
 TYR   0.012   0.002   TYR L  50 
 ARG   0.004   0.001   ARG L  19 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8792 (m-10) cc_final: 0.8222 (m-80)
REVERT: H   16 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8122 (mm-40)
REVERT: L  107 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8102 (tp)
  outliers start: 20
  outliers final: 13
  residues processed: 80
  average time/residue: 0.1498
  time to fit residues: 17.4738
Evaluate side-chains
  73 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  385 VAL
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  207 ILE
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  317 ILE
Chi-restraints excluded: chain H residue  106 TRP
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   76 ILE
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 68 optimal weight:    0.3980
   chunk 8 optimal weight:   20.0000
   chunk 27 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 11 optimal weight:    0.2980
   chunk 47 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   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 = 0.3503 r_free = 0.3503 target = 0.066171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.047549 restraints weight = 31789.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.048992 restraints weight = 16918.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.049912 restraints weight = 11487.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5998  Z= 0.146
  Angle     :  0.581   9.664   8266  Z= 0.283
  Chirality :  0.043   0.151    991
  Planarity :  0.003   0.031   1056
  Dihedral  :  8.023 140.518    942
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 20.00 %
    Favored  : 77.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.10 (0.30), residues: 843
  helix:  0.48 (0.36), residues: 227
  sheet: -0.96 (0.33), residues: 250
  loop : -1.23 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 155 
 HIS   0.002   0.001   HIS C 353 
 PHE   0.012   0.001   PHE H 105 
 TYR   0.009   0.001   TYR H 107 
 ARG   0.003   0.000   ARG C   7 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8719 (m-10) cc_final: 0.8110 (m-80)
REVERT: C  256 GLU cc_start: 0.8228 (tm-30) cc_final: 0.8007 (tm-30)
REVERT: L    5 MET cc_start: 0.8586 (tpp) cc_final: 0.8336 (tpp)
REVERT: L   24 CYS cc_start: 0.3410 (t) cc_final: 0.3166 (t)
REVERT: L   99 PHE cc_start: 0.8972 (m-80) cc_final: 0.8645 (m-80)
  outliers start: 13
  outliers final: 8
  residues processed: 78
  average time/residue: 0.1433
  time to fit residues: 15.8307
Evaluate side-chains
  72 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  385 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   95 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 60 optimal weight:    7.9990
   chunk 5 optimal weight:   20.0000
   chunk 3 optimal weight:   20.0000
   chunk 78 optimal weight:    7.9990
   chunk 49 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 1 optimal weight:    8.9990
   chunk 15 optimal weight:   50.0000
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.064926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.046213 restraints weight = 31737.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.047570 restraints weight = 16916.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.048450 restraints weight = 11628.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5998  Z= 0.226
  Angle     :  0.561   7.093   8266  Z= 0.281
  Chirality :  0.042   0.147    991
  Planarity :  0.003   0.029   1056
  Dihedral  :  8.074 140.637    942
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 21.09 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.92 (0.30), residues: 843
  helix:  0.81 (0.37), residues: 224
  sheet: -0.90 (0.33), residues: 252
  loop : -1.20 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 155 
 HIS   0.003   0.001   HIS C 353 
 PHE   0.021   0.002   PHE H  30 
 TYR   0.008   0.001   TYR L  50 
 ARG   0.003   0.000   ARG L  19 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8749 (m-10) cc_final: 0.8176 (m-80)
  outliers start: 15
  outliers final: 10
  residues processed: 74
  average time/residue: 0.1525
  time to fit residues: 16.0471
Evaluate side-chains
  71 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  385 VAL
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   76 ILE
Chi-restraints excluded: chain L residue   95 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 46 optimal weight:    0.0570
   chunk 59 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 82 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0870
   chunk 33 optimal weight:   10.0000
   chunk 78 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0670
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.4418

-------------------------------------------------------------------------------
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 = 0.3526 r_free = 0.3526 target = 0.067094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.048432 restraints weight = 31819.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.049917 restraints weight = 16771.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.050845 restraints weight = 11354.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.3329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   5998  Z= 0.134
  Angle     :  0.588  10.599   8266  Z= 0.281
  Chirality :  0.043   0.144    991
  Planarity :  0.003   0.032   1056
  Dihedral  :  7.854 140.536    942
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 22.17 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.56 (0.30), residues: 843
  helix:  1.18 (0.37), residues: 221
  sheet: -0.69 (0.32), residues: 256
  loop : -1.01 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 155 
 HIS   0.004   0.001   HIS C 353 
 PHE   0.018   0.001   PHE L  99 
 TYR   0.008   0.001   TYR H 107 
 ARG   0.003   0.000   ARG C   7 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8739 (m-10) cc_final: 0.8138 (m-80)
REVERT: C  256 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7807 (tm-30)
REVERT: C  257 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7815 (tm-30)
REVERT: L   99 PHE cc_start: 0.8654 (m-80) cc_final: 0.8428 (m-10)
  outliers start: 13
  outliers final: 10
  residues processed: 80
  average time/residue: 0.1436
  time to fit residues: 16.4265
Evaluate side-chains
  75 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  385 VAL
Chi-restraints excluded: chain C residue   30 HIS
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   95 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 82 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 74 optimal weight:   20.0000
   chunk 55 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
H  42 GLN
** L  91 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 = 0.3514 r_free = 0.3514 target = 0.066707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.047981 restraints weight = 31570.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.049461 restraints weight = 16565.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.050390 restraints weight = 11162.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5998  Z= 0.159
  Angle     :  0.560   7.349   8266  Z= 0.272
  Chirality :  0.042   0.142    991
  Planarity :  0.003   0.032   1056
  Dihedral  :  7.788 140.610    942
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 22.61 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.37 (0.30), residues: 843
  helix:  1.43 (0.37), residues: 217
  sheet: -0.63 (0.31), residues: 268
  loop : -0.90 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H 106 
 HIS   0.005   0.001   HIS C 353 
 PHE   0.014   0.001   PHE H 105 
 TYR   0.016   0.001   TYR R 403 
 ARG   0.002   0.000   ARG C   7 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8711 (m-10) cc_final: 0.8128 (m-80)
REVERT: L   24 CYS cc_start: 0.4430 (t) cc_final: 0.4114 (t)
  outliers start: 10
  outliers final: 9
  residues processed: 75
  average time/residue: 0.1359
  time to fit residues: 14.6091
Evaluate side-chains
  75 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  385 VAL
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   76 ILE
Chi-restraints excluded: chain L residue   95 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 81 optimal weight:    7.9990
   chunk 74 optimal weight:   20.0000
   chunk 34 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 70 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.064540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.045910 restraints weight = 32664.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.047257 restraints weight = 17709.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.048111 restraints weight = 12178.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5998  Z= 0.335
  Angle     :  0.633   9.030   8266  Z= 0.314
  Chirality :  0.043   0.149    991
  Planarity :  0.004   0.029   1056
  Dihedral  :  8.019 140.538    942
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 22.83 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.58 (0.30), residues: 843
  helix:  1.32 (0.37), residues: 224
  sheet: -0.79 (0.31), residues: 269
  loop : -1.08 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R 155 
 HIS   0.005   0.001   HIS C 353 
 PHE   0.028   0.002   PHE L  99 
 TYR   0.020   0.002   TYR R 403 
 ARG   0.003   0.000   ARG L  19 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8753 (m-10) cc_final: 0.8199 (m-80)
  outliers start: 11
  outliers final: 11
  residues processed: 66
  average time/residue: 0.1253
  time to fit residues: 12.3422
Evaluate side-chains
  69 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  385 VAL
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   76 ILE
Chi-restraints excluded: chain L residue   95 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 59 optimal weight:    7.9990
   chunk 76 optimal weight:    1.9990
   chunk 14 optimal weight:   30.0000
   chunk 62 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 74 optimal weight:   20.0000
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.065797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.047094 restraints weight = 32464.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.048411 restraints weight = 17432.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.049339 restraints weight = 12082.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5998  Z= 0.200
  Angle     :  0.610  10.187   8266  Z= 0.295
  Chirality :  0.043   0.156    991
  Planarity :  0.003   0.031   1056
  Dihedral  :  7.933 140.482    942
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 22.83 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.41 (0.30), residues: 843
  helix:  1.56 (0.37), residues: 221
  sheet: -0.77 (0.31), residues: 270
  loop : -0.96 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 155 
 HIS   0.003   0.001   HIS C 353 
 PHE   0.024   0.002   PHE L  99 
 TYR   0.023   0.001   TYR R 403 
 ARG   0.002   0.000   ARG C   7 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8748 (m-10) cc_final: 0.8180 (m-80)
REVERT: L   24 CYS cc_start: 0.4663 (t) cc_final: 0.4100 (t)
  outliers start: 12
  outliers final: 12
  residues processed: 73
  average time/residue: 0.1389
  time to fit residues: 14.6444
Evaluate side-chains
  75 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  385 VAL
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  207 ILE
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  317 ILE
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   76 ILE
Chi-restraints excluded: chain L residue   95 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 15 optimal weight:    0.3980
   chunk 82 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   chunk 77 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   chunk 21 optimal weight:    0.0270
   chunk 38 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.6642

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

Flipped N/Q/H residues before XYZ refinement:
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.067535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.049018 restraints weight = 32080.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.050483 restraints weight = 17033.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.051406 restraints weight = 11573.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5998  Z= 0.140
  Angle     :  0.600  11.845   8266  Z= 0.285
  Chirality :  0.042   0.155    991
  Planarity :  0.003   0.034   1056
  Dihedral  :  7.770 140.538    942
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 22.83 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 (0.30), residues: 843
  helix:  1.85 (0.37), residues: 217
  sheet: -0.57 (0.32), residues: 268
  loop : -0.83 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 155 
 HIS   0.003   0.000   HIS C 353 
 PHE   0.019   0.001   PHE L  99 
 TYR   0.022   0.001   TYR R 403 
 ARG   0.002   0.000   ARG C   7 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2110.73 seconds
wall clock time: 37 minutes 11.68 seconds (2231.68 seconds total)