Starting phenix.real_space_refine
on Tue Feb 11 15:45:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6u1n_20612/02_2025/6u1n_20612.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6u1n_20612/02_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_20612/02_2025/6u1n_20612.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6u1n_20612/02_2025/6u1n_20612.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6u1n_20612/02_2025/6u1n_20612.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6u1n_20612/02_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-5592/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: 4.02, per 1000 atoms: 0.69
  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: 1.90
  Conformation dependent library (CDL) restraints added in 959.3 milliseconds
  

  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: 0.80
  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: 2.00

  Time building geometry restraints manager: 2.01 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:             0.720
  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:                    0.050
  Process input model:                     18.050
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.900
-------------------------------------------------------------------------------
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  : 0.609 
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: 0.1636
  time to fit residues: 17.5212
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  : 0.639 
-------------------------------------------------------------------------------
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 = 0.046681 restraints weight = 31823.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.048121 restraints weight = 17006.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.049048 restraints weight = 11562.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
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  :  8.393 141.091    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  : 0.690 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8836 (m-80) cc_final: 0.8238 (m-80)
REVERT: R  397 ILE cc_start: 0.9495 (mt) cc_final: 0.9271 (pt)
REVERT: C  144 TYR cc_start: 0.8182 (m-80) cc_final: 0.7979 (m-80)
REVERT: H   16 GLN cc_start: 0.8307 (mm-40) cc_final: 0.8066 (mm-40)
REVERT: L   22 ILE cc_start: 0.9429 (mm) cc_final: 0.9208 (mt)
  outliers start: 12
  outliers final: 6
  residues processed: 83
  average time/residue: 0.1543
  time to fit residues: 17.7362
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  : 0.834 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 3 optimal weight:   20.0000
   chunk 72 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0000
   chunk 66 optimal weight:    1.9990
   chunk 33 optimal weight:   30.0000
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.5992

-------------------------------------------------------------------------------
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 = 0.3481 r_free = 0.3481 target = 0.065263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.046429 restraints weight = 31797.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.047898 restraints weight = 16843.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.048773 restraints weight = 11386.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5998  Z= 0.202
  Angle     :  0.568   7.872   8266  Z= 0.287
  Chirality :  0.043   0.171    991
  Planarity :  0.003   0.028   1056
  Dihedral  :  8.211 140.571    942
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 15.65 %
    Favored  : 80.87 %
  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: -2.04 (0.28), residues: 843
  helix: -0.36 (0.35), residues: 215
  sheet: -1.42 (0.31), residues: 261
  loop : -1.80 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 155 
 HIS   0.003   0.001   HIS C 353 
 PHE   0.016   0.001   PHE H 105 
 TYR   0.014   0.001   TYR R 403 
 ARG   0.003   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
  83 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8788 (m-80) cc_final: 0.8229 (m-80)
REVERT: H   16 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8058 (mm-40)
REVERT: L   22 ILE cc_start: 0.9458 (mm) cc_final: 0.9254 (mt)
  outliers start: 16
  outliers final: 9
  residues processed: 81
  average time/residue: 0.1530
  time to fit residues: 17.2657
Evaluate side-chains
  72 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 6 optimal weight:    0.9980
   chunk 4 optimal weight:   20.0000
   chunk 7 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   chunk 8 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 52 optimal weight:    9.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
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 = 0.3440 r_free = 0.3440 target = 0.063622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.044906 restraints weight = 32616.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.046286 restraints weight = 18131.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.047136 restraints weight = 12439.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   5998  Z= 0.340
  Angle     :  0.624   7.914   8266  Z= 0.319
  Chirality :  0.043   0.163    991
  Planarity :  0.004   0.029   1056
  Dihedral  :  8.348 140.566    942
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 16.74 %
    Favored  : 78.91 %
  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: -1.69 (0.29), residues: 843
  helix:  0.07 (0.36), residues: 218
  sheet: -1.23 (0.32), residues: 252
  loop : -1.69 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP H 106 
 HIS   0.003   0.001   HIS C 353 
 PHE   0.019   0.002   PHE H 105 
 TYR   0.011   0.002   TYR R 403 
 ARG   0.003   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  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8781 (m-10) cc_final: 0.8198 (m-80)
REVERT: H   16 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8105 (mm-40)
REVERT: L  107 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8109 (tp)
  outliers start: 20
  outliers final: 13
  residues processed: 80
  average time/residue: 0.1277
  time to fit residues: 14.8194
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  : 0.701 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 73 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0270
   chunk 8 optimal weight:   20.0000
   chunk 27 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0870
   chunk 47 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.6222

-------------------------------------------------------------------------------
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 = 43)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.047552 restraints weight = 31592.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.048991 restraints weight = 16647.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.049906 restraints weight = 11325.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5998  Z= 0.144
  Angle     :  0.578   9.751   8266  Z= 0.281
  Chirality :  0.043   0.150    991
  Planarity :  0.003   0.030   1056
  Dihedral  :  8.012 140.520    942
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 19.78 %
    Favored  : 77.83 %
  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:  0.46 (0.36), residues: 227
  sheet: -0.94 (0.33), residues: 250
  loop : -1.23 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 155 
 HIS   0.002   0.001   HIS C 210 
 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
  80 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8714 (m-10) cc_final: 0.8111 (m-80)
REVERT: C  256 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7995 (tm-30)
REVERT: L    5 MET cc_start: 0.8619 (tpp) cc_final: 0.8400 (tpp)
REVERT: L   24 CYS cc_start: 0.3373 (t) cc_final: 0.3124 (t)
REVERT: L   99 PHE cc_start: 0.8945 (m-80) cc_final: 0.8687 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 79
  average time/residue: 0.1435
  time to fit residues: 16.1674
Evaluate side-chains
  73 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
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   95 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 64 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9990
   chunk 5 optimal weight:    8.9990
   chunk 3 optimal weight:    9.9990
   chunk 78 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 15 optimal weight:   50.0000
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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 = 0.3450 r_free = 0.3450 target = 0.064023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.045454 restraints weight = 32125.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.046784 restraints weight = 17607.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.047580 restraints weight = 12172.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2776

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= 0.313
  Angle     :  0.596   6.257   8266  Z= 0.302
  Chirality :  0.043   0.148    991
  Planarity :  0.004   0.028   1056
  Dihedral  :  8.210 140.614    942
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 20.00 %
    Favored  : 75.43 %
  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: -1.06 (0.30), residues: 843
  helix:  0.70 (0.36), residues: 224
  sheet: -0.99 (0.33), residues: 252
  loop : -1.30 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP H 106 
 HIS   0.003   0.001   HIS C 353 
 PHE   0.020   0.002   PHE H  30 
 TYR   0.010   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
  83 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8765 (m-10) cc_final: 0.8203 (m-80)
  outliers start: 21
  outliers final: 15
  residues processed: 78
  average time/residue: 0.1253
  time to fit residues: 14.3941
Evaluate side-chains
  75 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
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   30 HIS
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 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 35 optimal weight:    8.9990
   chunk 33 optimal weight:    9.9990
   chunk 78 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    1.7990

-------------------------------------------------------------------------------
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 = 0.3477 r_free = 0.3477 target = 0.065020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.046332 restraints weight = 31868.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.047703 restraints weight = 17013.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.048610 restraints weight = 11668.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5998  Z= 0.207
  Angle     :  0.582  10.089   8266  Z= 0.286
  Chirality :  0.042   0.149    991
  Planarity :  0.003   0.030   1056
  Dihedral  :  8.068 140.498    942
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 21.09 %
    Favored  : 75.43 %
  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: -0.80 (0.30), residues: 843
  helix:  0.99 (0.36), residues: 224
  sheet: -0.91 (0.32), residues: 257
  loop : -1.12 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 155 
 HIS   0.004   0.001   HIS C 353 
 PHE   0.016   0.001   PHE H 105 
 TYR   0.007   0.001   TYR L  92 
 ARG   0.002   0.000   ARG C  25 

*********************** 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: 16
    poor density    : 66
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8736 (m-10) cc_final: 0.8166 (m-80)
REVERT: C  256 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7758 (tm-30)
REVERT: L   99 PHE cc_start: 0.9032 (m-80) cc_final: 0.8708 (m-80)
  outliers start: 16
  outliers final: 13
  residues processed: 79
  average time/residue: 0.1475
  time to fit residues: 16.3859
Evaluate side-chains
  77 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
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   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 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   98 THR
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:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 74 optimal weight:   20.0000
   chunk 55 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3500 r_free = 0.3500 target = 0.066095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.047315 restraints weight = 31629.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.048749 restraints weight = 16721.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.049654 restraints weight = 11353.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.3240

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= 0.159
  Angle     :  0.567   8.134   8266  Z= 0.277
  Chirality :  0.042   0.142    991
  Planarity :  0.003   0.031   1056
  Dihedral  :  7.929 140.544    942
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  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: -0.56 (0.30), residues: 843
  helix:  1.27 (0.37), residues: 224
  sheet: -0.82 (0.32), residues: 258
  loop : -0.98 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 155 
 HIS   0.003   0.001   HIS C 353 
 PHE   0.013   0.001   PHE H 105 
 TYR   0.014   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
  75 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8711 (m-10) cc_final: 0.8121 (m-80)
REVERT: H   15 VAL cc_start: 0.9120 (t) cc_final: 0.8799 (m)
REVERT: L   24 CYS cc_start: 0.4500 (t) cc_final: 0.4159 (t)
REVERT: L   99 PHE cc_start: 0.8983 (m-80) cc_final: 0.8690 (m-80)
  outliers start: 9
  outliers final: 8
  residues processed: 74
  average time/residue: 0.1375
  time to fit residues: 14.7856
Evaluate side-chains
  73 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
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   95 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   chunk 48 optimal weight:    8.9990
   chunk 30 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 37 optimal weight:    8.9990
   chunk 70 optimal weight:    0.8980
   chunk 9 optimal weight:    7.9990
   overall best weight:    3.9788

-------------------------------------------------------------------------------
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 = 0.3444 r_free = 0.3444 target = 0.063704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.045023 restraints weight = 32660.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.046265 restraints weight = 17967.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.047139 restraints weight = 12537.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.3009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   5998  Z= 0.400
  Angle     :  0.659   8.459   8266  Z= 0.333
  Chirality :  0.043   0.147    991
  Planarity :  0.004   0.029   1056
  Dihedral  :  8.196 140.543    942
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 21.30 %
    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: -0.76 (0.30), residues: 843
  helix:  1.12 (0.37), residues: 224
  sheet: -0.96 (0.33), residues: 249
  loop : -1.12 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP H 106 
 HIS   0.003   0.001   HIS C 353 
 PHE   0.021   0.002   PHE H 105 
 TYR   0.019   0.002   TYR R 403 
 ARG   0.003   0.001   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
  76 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8783 (m-10) cc_final: 0.8254 (m-80)
REVERT: H   15 VAL cc_start: 0.9158 (t) cc_final: 0.8865 (m)
  outliers start: 17
  outliers final: 16
  residues processed: 72
  average time/residue: 0.1293
  time to fit residues: 13.7772
Evaluate side-chains
  74 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
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   30 HIS
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   59 VAL
Chi-restraints excluded: chain L residue   76 ILE
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 14 optimal weight:   30.0000
   chunk 62 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 74 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
L  91 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.065229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.046274 restraints weight = 31958.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.047621 restraints weight = 17004.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.048559 restraints weight = 11685.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.3190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5998  Z= 0.206
  Angle     :  0.620  10.167   8266  Z= 0.301
  Chirality :  0.043   0.151    991
  Planarity :  0.003   0.031   1056
  Dihedral  :  8.067 140.488    942
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 23.04 %
    Favored  : 74.35 %
  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:  1.34 (0.37), residues: 224
  sheet: -0.86 (0.32), residues: 259
  loop : -1.03 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 155 
 HIS   0.003   0.001   HIS C 353 
 PHE   0.017   0.001   PHE H 105 
 TYR   0.018   0.001   TYR R 403 
 ARG   0.003   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  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  119 PHE cc_start: 0.8749 (m-10) cc_final: 0.8183 (m-80)
REVERT: H   15 VAL cc_start: 0.9181 (t) cc_final: 0.8882 (m)
REVERT: L   24 CYS cc_start: 0.4317 (t) cc_final: 0.3552 (t)
REVERT: L   99 PHE cc_start: 0.9085 (m-80) cc_final: 0.8823 (m-80)
  outliers start: 12
  outliers final: 10
  residues processed: 74
  average time/residue: 0.1299
  time to fit residues: 14.0931
Evaluate side-chains
  74 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
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   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   49 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:    4.9990
   chunk 15 optimal weight:   20.0000
   chunk 82 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 77 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0770
   chunk 1 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 24 optimal weight:   10.0000
   overall best weight:    0.6940

-------------------------------------------------------------------------------
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 = 0.3519 r_free = 0.3519 target = 0.066815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.048025 restraints weight = 32011.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.049473 restraints weight = 16802.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.050398 restraints weight = 11360.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5998  Z= 0.149
  Angle     :  0.613  10.861   8266  Z= 0.294
  Chirality :  0.043   0.184    991
  Planarity :  0.003   0.034   1056
  Dihedral  :  7.870 140.534    942
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  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: -0.27 (0.30), residues: 843
  helix:  1.68 (0.37), residues: 217
  sheet: -0.75 (0.32), residues: 261
  loop : -0.80 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 155 
 HIS   0.003   0.001   HIS C 353 
 PHE   0.011   0.001   PHE L  99 
 TYR   0.022   0.001   TYR R 403 
 ARG   0.003   0.000   ARG C   7 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2040.11 seconds
wall clock time: 37 minutes 13.18 seconds (2233.18 seconds total)