Starting phenix.real_space_refine
on Tue Jul 29 18:20:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rme_19359/07_2025/8rme_19359.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rme_19359/07_2025/8rme_19359.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rme_19359/07_2025/8rme_19359.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rme_19359/07_2025/8rme_19359.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rme_19359/07_2025/8rme_19359.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rme_19359/07_2025/8rme_19359.cif"
  }
  resolution = 2.49
  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=   0.001 sd=   0.038
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Fe      2      7.16       5
     P       4      5.49       5
     S      59      5.16       5
     C    7287      2.51       5
     N    2016      2.21       5
     O    2394      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11762
  Number of models: 1
  Model: ""
    Number of chains: 19
    Chain: "A"
      Number of atoms: 3140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 3140
          Classifications: {'peptide': 401}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 381}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'LLP:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 678
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 678
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "D"
      Number of atoms: 939
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 123, 927
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 4, 'TRANS': 118}
      Conformer: "B"
        Number of residues, atoms: 123, 927
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 4, 'TRANS': 118}
          bond proxies already assigned to first conformer: 927
    Chain: "I"
      Number of atoms: 927
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 927
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 4, 'TRANS': 112}
    Chain: "C"
      Number of atoms: 576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 576
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
    Chain: "E"
      Number of atoms: 3082
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 392, 3057
          Classifications: {'peptide': 392}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 372}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'LLP:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
      Conformer: "B"
        Number of residues, atoms: 392, 3057
          Classifications: {'peptide': 392}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 372}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'LLP:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
          bond proxies already assigned to first conformer: 3085
    Chain: "F"
      Number of atoms: 678
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 678
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "G"
      Number of atoms: 576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 576
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
    Chain: "H"
      Number of atoms: 939
      Number of conformers: 2
      Conformer: "B"
        Number of residues, atoms: 123, 927
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 4, 'TRANS': 118}
      Conformer: "D"
        Number of residues, atoms: 123, 927
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 4, 'TRANS': 118}
          bond proxies already assigned to first conformer: 927
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'FE2': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 34
          Unusual residues: {'8Q1': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
    Chain: "G"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 34
          Unusual residues: {'8Q1': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
    Chain: "H"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'FE2': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 64
          Classifications: {'water': 64}
          Link IDs: {None: 63}
    Chain: "B"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "D"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "I"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "E"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 69
          Classifications: {'water': 69}
          Link IDs: {None: 68}
    Chain: "F"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2529  SG  CYS A 381      33.522  42.781  65.744  1.00102.83           S
  ATOM   4296  SG  CYS D  95      33.489  39.567  63.999  1.00 79.99           S
  ATOM   8808  SG  CYS E 381      73.719  95.939  65.659  1.00 94.31           S
  ATOM  11074  SG  CYS H  95      73.374  98.637  63.467  1.00 67.25           S

  Residues with excluded nonbonded symmetry interactions: 5
    residue:
      pdb=" N  ATYR D  35 " occ=0.55
      ... (22 atoms not shown)
      pdb=" OH BTYR D  35 " occ=0.45
    residue:
      pdb=" N  AASN E  83 " occ=0.46
      ... (14 atoms not shown)
      pdb=" ND2BASN E  83 " occ=0.54
    residue:
      pdb=" N  AARG E 321 " occ=0.63
      ... (20 atoms not shown)
      pdb=" NH2BARG E 321 " occ=0.37
    residue:
      pdb=" N  ACYS E 426 " occ=0.26
      ... (10 atoms not shown)
      pdb=" SG BCYS E 426 " occ=0.74
    residue:
      pdb=" N  BTYR H  35 " occ=0.82
      ... (22 atoms not shown)
      pdb=" OH DTYR H  35 " occ=0.18
  Time building chain proxies: 10.51, per 1000 atoms: 0.89
  Number of scatterers: 11762
  At special positions: 0
  Unit cell: (107.64, 142.416, 104.328, 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)
     Fe      2     26.01
     S      59     16.00
     P       4     15.00
     O    2394      8.00
     N    2016      7.00
     C    7287      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.06
  Conformation dependent library (CDL) restraints added in 3.7 seconds
  

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2750

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 9 sheets defined
      55.5% alpha, 10.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 83
      Proline residue:  A  79  - end of helix
    Processing helix  chain 'A' and resid 93 through 115
    Processing helix  chain 'A' and resid 117 through 119
      No H-bonds generated for 'chain 'A' and resid 117 through 119'
    Processing helix  chain 'A' and resid 126 through 142
    Processing helix  chain 'A' and resid 156 through 169
    Processing helix  chain 'A' and resid 185 through 193
      removed outlier: 3.541A  pdb=" N   ILE A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 226
    Processing helix  chain 'A' and resid 257 through 259
      No H-bonds generated for 'chain 'A' and resid 257 through 259'
    Processing helix  chain 'A' and resid 297 through 337
      removed outlier: 5.655A  pdb=" N   GLU A 316 " --> pdb=" O   GLN A 312 " (cutoff:3.500A)
      removed outlier: 5.769A  pdb=" N   TYR A 317 " --> pdb=" O   GLN A 313 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   SER A 336 " --> pdb=" O   ASN A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 349
      removed outlier: 4.002A  pdb=" N   HIS A 349 " --> pdb=" O   PRO A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 370
    Processing helix  chain 'A' and resid 389 through 395
    Processing helix  chain 'A' and resid 398 through 403
      removed outlier: 3.587A  pdb=" N   ALA A 402 " --> pdb=" O   GLU A 399 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   HIS A 403 " --> pdb=" O   ASP A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 437
    Processing helix  chain 'A' and resid 437 through 445
      removed outlier: 3.738A  pdb=" N   GLU A 441 " --> pdb=" O   SER A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 452
      removed outlier: 3.507A  pdb=" N   SER A 451 " --> pdb=" O   ASP A 448 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE A 452 " --> pdb=" O   LEU A 449 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 448 through 452'
    Processing helix  chain 'B' and resid 6 through 21
    Processing helix  chain 'B' and resid 25 through 43
    Processing helix  chain 'B' and resid 48 through 76
    Processing helix  chain 'B' and resid 81 through 85
      removed outlier: 3.673A  pdb=" N   ASN B  85 " --> pdb=" O   ILE B  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 45
      removed outlier: 4.084A  pdb=" N   HIS D  42 " --> pdb=" O   LYS D  38 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   TYR D  43 " --> pdb=" O   VAL D  39 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 95 through 109
    Processing helix  chain 'D' and resid 113 through 119
      removed outlier: 4.062A  pdb=" N   THR D 119 " --> pdb=" O   GLU D 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 121 through 130
    Processing helix  chain 'D' and resid 132 through 134
      No H-bonds generated for 'chain 'D' and resid 132 through 134'
    Processing helix  chain 'D' and resid 135 through 157
      removed outlier: 3.941A  pdb=" N   SER D 139 " --> pdb=" O   LYS D 135 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 91 through 113
    Processing helix  chain 'I' and resid 181 through 195
    Processing helix  chain 'C' and resid 4 through 17
    Processing helix  chain 'C' and resid 36 through 52
    Processing helix  chain 'C' and resid 56 through 63
    Processing helix  chain 'C' and resid 65 through 76
    Processing helix  chain 'E' and resid 70 through 83
      Proline residue:  E  79  - end of helix
    Processing helix  chain 'E' and resid 93 through 115
      removed outlier: 3.578A  pdb=" N   ILE E 114 " --> pdb=" O   VAL E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 117 through 119
      No H-bonds generated for 'chain 'E' and resid 117 through 119'
    Processing helix  chain 'E' and resid 126 through 142
    Processing helix  chain 'E' and resid 156 through 168
    Processing helix  chain 'E' and resid 185 through 193
    Processing helix  chain 'E' and resid 214 through 225
    Processing helix  chain 'E' and resid 257 through 259
      No H-bonds generated for 'chain 'E' and resid 257 through 259'
    Processing helix  chain 'E' and resid 297 through 337
      removed outlier: 5.449A  pdb=" N   GLU E 316 " --> pdb=" O   GLN E 312 " (cutoff:3.500A)
      removed outlier: 5.504A  pdb=" N   TYR E 317 " --> pdb=" O   GLN E 313 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 345 through 349
      removed outlier: 3.859A  pdb=" N   HIS E 349 " --> pdb=" O   PRO E 346 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 362 through 370
    Processing helix  chain 'E' and resid 379 through 383
    Processing helix  chain 'E' and resid 389 through 395
    Processing helix  chain 'E' and resid 398 through 403
    Processing helix  chain 'E' and resid 415 through 437
    Processing helix  chain 'E' and resid 437 through 445
    Processing helix  chain 'F' and resid 6 through 21
    Processing helix  chain 'F' and resid 25 through 43
    Processing helix  chain 'F' and resid 48 through 76
    Processing helix  chain 'F' and resid 81 through 85
    Processing helix  chain 'G' and resid 4 through 17
    Processing helix  chain 'G' and resid 36 through 51
    Processing helix  chain 'G' and resid 56 through 63
    Processing helix  chain 'G' and resid 65 through 76
    Processing helix  chain 'H' and resid 36 through 45
    Processing helix  chain 'H' and resid 95 through 110
    Processing helix  chain 'H' and resid 113 through 118
    Processing helix  chain 'H' and resid 121 through 130
      removed outlier: 3.512A  pdb=" N   ILE H 125 " --> pdb=" O   LYS H 121 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 132 through 134
      No H-bonds generated for 'chain 'H' and resid 132 through 134'
    Processing helix  chain 'H' and resid 135 through 157
      removed outlier: 4.032A  pdb=" N   SER H 139 " --> pdb=" O   LYS H 135 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60
      removed outlier: 6.846A  pdb=" N   LEU A  59 " --> pdb=" O   ALA A 374 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124
      removed outlier: 6.855A  pdb=" N   SER A 198 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   HIS A 230 " --> pdb=" O   SER A 198 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   VAL A 200 " --> pdb=" O   HIS A 230 " (cutoff:3.500A)
      removed outlier: 7.844A  pdb=" N   ASP A 232 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   HIS A 148 " --> pdb=" O   SER A 198 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   VAL A 200 " --> pdb=" O   HIS A 148 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   ILE A 150 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LEU A 149 " --> pdb=" O   THR A 174 " (cutoff:3.500A)
      removed outlier: 7.476A  pdb=" N   LEU A 176 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   THR A 151 " --> pdb=" O   LEU A 176 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 340 through 342
      removed outlier: 3.666A  pdb=" N   SER A 376 " --> pdb=" O   ARG A 407 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 65
      removed outlier: 3.826A  pdb=" N   ASP D  87 " --> pdb=" O   GLN D  78 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'I' and resid 124 through 128
      removed outlier: 3.724A  pdb=" N   VAL I 144 " --> pdb=" O   SER I 157 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 59 through 60
      removed outlier: 6.830A  pdb=" N   LEU E  59 " --> pdb=" O   ALA E 374 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 121 through 124
      removed outlier: 6.818A  pdb=" N   SER E 198 " --> pdb=" O   TYR E 228 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   HIS E 230 " --> pdb=" O   SER E 198 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   VAL E 200 " --> pdb=" O   HIS E 230 " (cutoff:3.500A)
      removed outlier: 7.730A  pdb=" N   ASP E 232 " --> pdb=" O   VAL E 200 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   HIS E 148 " --> pdb=" O   SER E 198 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   VAL E 200 " --> pdb=" O   HIS E 148 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ILE E 150 " --> pdb=" O   VAL E 200 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   LEU E 149 " --> pdb=" O   THR E 174 " (cutoff:3.500A)
      removed outlier: 7.514A  pdb=" N   LEU E 176 " --> pdb=" O   LEU E 149 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   THR E 151 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 340 through 342
      removed outlier: 3.678A  pdb=" N   SER E 376 " --> pdb=" O   ARG E 407 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 59 through 65
      removed outlier: 3.563A  pdb=" N   ASP H  87 " --> pdb=" O   GLN H  78 " (cutoff:3.500A)

    641 hydrogen bonds defined for protein.
    1871 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: 4.33

  Time building geometry restraints manager: 3.61 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1982
        1.30 -     1.43: 2876
        1.43 -     1.56: 6834
        1.56 -     1.69: 5
        1.69 -     1.82: 95
  Bond restraints: 11792
  Sorted by residual:
  bond pdb=" NZ  LLP E 258 "
       pdb=" C4' LLP E 258 "
    ideal  model  delta    sigma   weight residual
    1.273  1.430 -0.157 2.00e-02 2.50e+03 6.14e+01
  bond pdb=" NZ  LLP A 258 "
       pdb=" C4' LLP A 258 "
    ideal  model  delta    sigma   weight residual
    1.273  1.429 -0.156 2.00e-02 2.50e+03 6.12e+01
  bond pdb=" OP4 LLP A 258 "
       pdb=" P   LLP A 258 "
    ideal  model  delta    sigma   weight residual
    1.726  1.609  0.117 2.00e-02 2.50e+03 3.40e+01
  bond pdb=" OP4 LLP E 258 "
       pdb=" P   LLP E 258 "
    ideal  model  delta    sigma   weight residual
    1.726  1.610  0.116 2.00e-02 2.50e+03 3.38e+01
  bond pdb=" C   PRO E  71 "
       pdb=" O   PRO E  71 "
    ideal  model  delta    sigma   weight residual
    1.238  1.179  0.058 1.24e-02 6.50e+03 2.21e+01
  ... (remaining 11787 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.11: 15821
        4.11 -     8.21: 101
        8.21 -    12.32: 3
       12.32 -    16.43: 0
       16.43 -    20.54: 1
  Bond angle restraints: 15926
  Sorted by residual:
  angle pdb=" NZ  LLP E 258 "
        pdb=" C4' LLP E 258 "
        pdb=" C4  LLP E 258 "
      ideal   model   delta    sigma   weight residual
     120.09   99.55   20.54 3.00e+00 1.11e-01 4.69e+01
  angle pdb=" CA  ARG E 273 "
        pdb=" C   ARG E 273 "
        pdb=" O   ARG E 273 "
      ideal   model   delta    sigma   weight residual
     120.63  113.72    6.91 1.05e+00 9.07e-01 4.33e+01
  angle pdb=" CA  ARG E 273 "
        pdb=" C   ARG E 273 "
        pdb=" N   PRO E 274 "
      ideal   model   delta    sigma   weight residual
     118.05  123.97   -5.92 9.50e-01 1.11e+00 3.89e+01
  angle pdb=" N   LEU D 155 "
        pdb=" CA  LEU D 155 "
        pdb=" C   LEU D 155 "
      ideal   model   delta    sigma   weight residual
     111.07  117.55   -6.48 1.07e+00 8.73e-01 3.67e+01
  angle pdb=" N   GLU A 435 "
        pdb=" CA  GLU A 435 "
        pdb=" C   GLU A 435 "
      ideal   model   delta    sigma   weight residual
     112.89  105.46    7.43 1.24e+00 6.50e-01 3.59e+01
  ... (remaining 15921 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.67: 6854
       32.67 -    65.33: 330
       65.33 -    98.00: 44
       98.00 -   130.67: 1
      130.67 -   163.33: 8
  Dihedral angle restraints: 7237
    sinusoidal: 2966
      harmonic: 4271
  Sorted by residual:
  dihedral pdb=" C37 8Q1 C 101 "
           pdb=" C38 8Q1 C 101 "
           pdb=" C39 8Q1 C 101 "
           pdb=" O40 8Q1 C 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -114.72   48.61 -163.33     1      3.00e+01 1.11e-03 2.09e+01
  dihedral pdb=" C37 8Q1 C 101 "
           pdb=" C38 8Q1 C 101 "
           pdb=" C39 8Q1 C 101 "
           pdb=" N41 8Q1 C 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
      64.60 -133.17 -162.23     1      3.00e+01 1.11e-03 2.08e+01
  dihedral pdb=" C39 8Q1 C 101 "
           pdb=" C42 8Q1 C 101 "
           pdb=" N41 8Q1 C 101 "
           pdb=" C43 8Q1 C 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
      89.93  -66.27  156.20     1      3.00e+01 1.11e-03 2.04e+01
  ... (remaining 7234 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1451
       0.062 -    0.123: 265
       0.123 -    0.185: 58
       0.185 -    0.246: 21
       0.246 -    0.308: 6
  Chirality restraints: 1801
  Sorted by residual:
  chirality pdb=" CA  ASP A 339 "
            pdb=" N   ASP A 339 "
            pdb=" C   ASP A 339 "
            pdb=" CB  ASP A 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.37e+00
  chirality pdb=" CA  ASP E 339 "
            pdb=" N   ASP E 339 "
            pdb=" C   ASP E 339 "
            pdb=" CB  ASP E 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" CB  VAL E  73 "
            pdb=" CA  VAL E  73 "
            pdb=" CG1 VAL E  73 "
            pdb=" CG2 VAL E  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.19e+00
  ... (remaining 1798 not shown)

  Planarity restraints: 2049
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CE  LLP A 258 "    0.010 2.00e-02 2.50e+03   2.93e-01 8.61e+02
        pdb=" NZ  LLP A 258 "    0.231 2.00e-02 2.50e+03
        pdb=" C4  LLP A 258 "    0.241 2.00e-02 2.50e+03
        pdb=" C4' LLP A 258 "   -0.482 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C32 8Q1 G 101 "   -0.069 2.00e-02 2.50e+03   7.98e-02 7.97e+01
        pdb=" C34 8Q1 G 101 "    0.014 2.00e-02 2.50e+03
        pdb=" C37 8Q1 G 101 "   -0.097 2.00e-02 2.50e+03
        pdb=" N36 8Q1 G 101 "    0.131 2.00e-02 2.50e+03
        pdb=" O35 8Q1 G 101 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C38 8Q1 G 101 "    0.053 2.00e-02 2.50e+03   5.75e-02 4.14e+01
        pdb=" C39 8Q1 G 101 "   -0.020 2.00e-02 2.50e+03
        pdb=" C42 8Q1 G 101 "    0.070 2.00e-02 2.50e+03
        pdb=" N41 8Q1 G 101 "   -0.091 2.00e-02 2.50e+03
        pdb=" O40 8Q1 G 101 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 2046 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 159
        2.64 -     3.20: 10352
        3.20 -     3.77: 19118
        3.77 -     4.33: 28302
        4.33 -     4.90: 44649
  Nonbonded interactions: 102580
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D  71 "
            pdb="FE   FE2 D 201 "
     model   vdw
     2.073 3.000
  nonbonded pdb=" O   SER E 365 "
            pdb=" OH  TYR H  43 "
     model   vdw
     2.086 3.040
  nonbonded pdb=" OD2 ASP D  71 "
            pdb="FE   FE2 D 201 "
     model   vdw
     2.140 3.000
  nonbonded pdb=" OD1 ASP H  71 "
            pdb="FE   FE2 H 201 "
     model   vdw
     2.192 3.000
  nonbonded pdb=" OE1 GLN E 312 "
            pdb=" O   HOH E 601 "
     model   vdw
     2.204 3.040
  ... (remaining 102575 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 56 through 82 or resid 84 through 320 or resid 322 through \ 
 425 or resid 427 through 447))
  selection = (chain 'E' and (resid 56 through 82 or resid 84 through 320 or resid 322 through \ 
 382 or resid 384 through 425 or resid 427 through 447))
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and (resid 36 through 157 or resid 201))
  selection = (chain 'H' and (resid 36 through 157 or resid 201))
}

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=0.18 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     35.840
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.060
  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:15.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
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      :  0.006   0.157  11794  Z= 0.389
  Angle     :  0.859  20.537  15926  Z= 0.561
  Chirality :  0.057   0.308   1801
  Planarity :  0.008   0.293   2049
  Dihedral  : 19.047 163.335   4487
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 18.82 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.22), residues: 1451
  helix:  0.81 (0.18), residues: 794
  sheet:  0.18 (0.38), residues: 203
  loop : -0.45 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E 440 
 HIS   0.017   0.002   HIS B  71 
 PHE   0.020   0.002   PHE F  40 
 TYR   0.016   0.002   TYR A 350 
 ARG   0.004   0.000   ARG E 292 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16070 (  641)
  hydrogen bonds       : angle       5.97382 ( 1871)
  covalent geometry    : bond        0.00641 (11792)
  covalent geometry    : angle       0.85928 (15926)
  Misc. bond           : bond        0.03136 (    2)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 164
  time to evaluate  : 1.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ARG cc_start: 0.7549 (mtm110) cc_final: 0.6723 (pmt170)
REVERT: A  226 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7991 (mtmm)
REVERT: A  321 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7771 (mtp180)
REVERT: A  347 LYS cc_start: 0.8240 (mttm) cc_final: 0.7913 (mtmt)
REVERT: A  417 GLU cc_start: 0.7621 (tt0) cc_final: 0.7250 (mp0)
REVERT: D  118 LEU cc_start: 0.7788 (mt) cc_final: 0.7429 (mp)
REVERT: I  148 GLN cc_start: 0.8206 (tp-100) cc_final: 0.8000 (mm-40)
REVERT: E   91 ARG cc_start: 0.8258 (mtp-110) cc_final: 0.7884 (mtt-85)
REVERT: E  144 SER cc_start: 0.8637 (p) cc_final: 0.8402 (p)
REVERT: E  145 ARG cc_start: 0.7082 (mtm110) cc_final: 0.6514 (pmt170)
REVERT: E  275 ARG cc_start: 0.7460 (tpp-160) cc_final: 0.7228 (tpt-90)
REVERT: E  327 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7264 (mt-10)
REVERT: E  417 GLU cc_start: 0.7817 (tt0) cc_final: 0.7296 (mp0)
REVERT: F   18 ARG cc_start: 0.7510 (mtm-85) cc_final: 0.7170 (mtt-85)
REVERT: F   42 GLU cc_start: 0.7686 (tt0) cc_final: 0.7148 (mt-10)
REVERT: F   51 GLU cc_start: 0.7516 (tp30) cc_final: 0.7174 (tm-30)
REVERT: F   71 HIS cc_start: 0.7721 (t-90) cc_final: 0.7452 (t-90)
REVERT: H  157 GLN cc_start: 0.6140 (OUTLIER) cc_final: 0.5910 (mt0)
  outliers start: 19
  outliers final: 9
  residues processed: 178
  average time/residue: 2.0151
  time to fit residues: 383.6453
Evaluate side-chains
  155 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 144
  time to evaluate  : 1.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  321 ARG
Chi-restraints excluded: chain A residue  400 ASP
Chi-restraints excluded: chain D residue  139 SER
Chi-restraints excluded: chain E residue  443 VAL
Chi-restraints excluded: chain G residue    4 ILE
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   41 ASP
Chi-restraints excluded: chain H residue  157 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 121 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9990
   chunk 60 optimal weight:    9.9990
   chunk 37 optimal weight:    0.8980
   chunk 73 optimal weight:   10.0000
   chunk 58 optimal weight:   10.0000
   chunk 112 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 68 optimal weight:   10.0000
   chunk 84 optimal weight:    1.9990
   chunk 130 optimal weight:   10.0000
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 456 GLN
** B  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 151 ASN
E 179 GLN
E 194 GLN
E 207 ASN
E 245 ASN
G  20 GLN
G  25 ASN
H 157 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.154457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.096328 restraints weight = 38207.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 3.01
r_work: 0.3138 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3121
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.1124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11794  Z= 0.152
  Angle     :  0.531   8.208  15926  Z= 0.283
  Chirality :  0.044   0.173   1801
  Planarity :  0.004   0.051   2049
  Dihedral  : 11.250 169.002   1693
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 18.10 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  1.19 (0.22), residues: 1451
  helix:  1.56 (0.19), residues: 798
  sheet:  0.32 (0.38), residues: 203
  loop : -0.26 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 108 
 HIS   0.004   0.001   HIS E 319 
 PHE   0.010   0.002   PHE H  93 
 TYR   0.014   0.002   TYR E  80 
 ARG   0.006   0.000   ARG H  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05259 (  641)
  hydrogen bonds       : angle       4.55026 ( 1871)
  covalent geometry    : bond        0.00352 (11792)
  covalent geometry    : angle       0.53150 (15926)
  Misc. bond           : bond        0.00047 (    2)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 2.337 
Fit side-chains
   revert: symmetry clash
REVERT: A  226 LYS cc_start: 0.8535 (mtpt) cc_final: 0.8255 (mtmm)
REVERT: A  347 LYS cc_start: 0.8459 (mttm) cc_final: 0.8120 (mtmt)
REVERT: A  417 GLU cc_start: 0.7826 (tt0) cc_final: 0.7488 (mp0)
REVERT: B   41 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7857 (ttm170)
REVERT: B   71 HIS cc_start: 0.8155 (t-90) cc_final: 0.7875 (t-170)
REVERT: D   89 ARG cc_start: 0.8001 (mmt90) cc_final: 0.7098 (mmp80)
REVERT: E   91 ARG cc_start: 0.8711 (mtp-110) cc_final: 0.8225 (mtt-85)
REVERT: E  144 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8395 (p)
REVERT: E  145 ARG cc_start: 0.7518 (mtm110) cc_final: 0.6837 (pmt170)
REVERT: E  247 MET cc_start: 0.8966 (mtt) cc_final: 0.8593 (mtt)
REVERT: E  275 ARG cc_start: 0.8190 (tpp-160) cc_final: 0.7713 (tpt-90)
REVERT: E  347 LYS cc_start: 0.7781 (mmtt) cc_final: 0.7578 (mmtt)
REVERT: E  417 GLU cc_start: 0.7996 (tt0) cc_final: 0.7456 (mp0)
REVERT: F   18 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.7552 (mtm-85)
REVERT: F   71 HIS cc_start: 0.7902 (t-90) cc_final: 0.7695 (t-90)
REVERT: H  118 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7725 (mm)
  outliers start: 24
  outliers final: 9
  residues processed: 165
  average time/residue: 2.1293
  time to fit residues: 375.1209
Evaluate side-chains
  152 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 1.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue   41 ARG
Chi-restraints excluded: chain I residue  174 VAL
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain E residue   61 MET
Chi-restraints excluded: chain E residue  144 SER
Chi-restraints excluded: chain H residue   41 ASP
Chi-restraints excluded: chain H residue   79 VAL
Chi-restraints excluded: chain H residue  118 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 136 optimal weight:    5.9990
   chunk 105 optimal weight:    4.9990
   chunk 103 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** B  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.150068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.087335 restraints weight = 44597.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 3.66
r_work: 0.2852 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2853
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2853
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11794  Z= 0.143
  Angle     :  0.499   7.828  15926  Z= 0.266
  Chirality :  0.043   0.166   1801
  Planarity :  0.004   0.047   2049
  Dihedral  :  9.265 145.663   1677
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 18.26 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  1.44 (0.23), residues: 1451
  helix:  1.79 (0.19), residues: 798
  sheet:  0.43 (0.39), residues: 201
  loop : -0.22 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 108 
 HIS   0.005   0.001   HIS F  71 
 PHE   0.009   0.002   PHE H  93 
 TYR   0.014   0.002   TYR A 260 
 ARG   0.003   0.000   ARG H  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05050 (  641)
  hydrogen bonds       : angle       4.39503 ( 1871)
  covalent geometry    : bond        0.00332 (11792)
  covalent geometry    : angle       0.49927 (15926)
  Misc. bond           : bond        0.00048 (    2)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 142
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
REVERT: A  226 LYS cc_start: 0.8459 (mtpt) cc_final: 0.7982 (mtmm)
REVERT: A  347 LYS cc_start: 0.8175 (mttm) cc_final: 0.7730 (mtmt)
REVERT: A  364 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7389 (tm-30)
REVERT: A  417 GLU cc_start: 0.7778 (tt0) cc_final: 0.7086 (mp0)
REVERT: B   18 ARG cc_start: 0.7860 (mtt90) cc_final: 0.7532 (mtt90)
REVERT: B   41 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8212 (mtt90)
REVERT: D   89 ARG cc_start: 0.7603 (mmt90) cc_final: 0.6592 (mmp80)
REVERT: I  164 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7443 (mttt)
REVERT: E  145 ARG cc_start: 0.7402 (mtm110) cc_final: 0.6511 (pmt170)
REVERT: E  247 MET cc_start: 0.8773 (mtt) cc_final: 0.8355 (mtt)
REVERT: E  275 ARG cc_start: 0.7921 (tpp-160) cc_final: 0.7407 (tpt-90)
REVERT: E  347 LYS cc_start: 0.7548 (mmtt) cc_final: 0.7324 (mmtt)
REVERT: E  417 GLU cc_start: 0.7787 (tt0) cc_final: 0.6945 (mp0)
REVERT: F   71 HIS cc_start: 0.7941 (t-90) cc_final: 0.7700 (t-90)
REVERT: H  118 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7261 (mm)
  outliers start: 29
  outliers final: 9
  residues processed: 162
  average time/residue: 1.6688
  time to fit residues: 290.0581
Evaluate side-chains
  151 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 1.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  441 GLU
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue   41 ARG
Chi-restraints excluded: chain I residue  164 LYS
Chi-restraints excluded: chain I residue  174 VAL
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   79 VAL
Chi-restraints excluded: chain H residue  118 LEU
Chi-restraints excluded: chain H residue  136 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 143 optimal weight:   10.0000
   chunk 50 optimal weight:    9.9990
   chunk 37 optimal weight:    0.5980
   chunk 101 optimal weight:    5.9990
   chunk 44 optimal weight:    0.0470
   chunk 76 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    1.1082

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

Flipped N/Q/H residues before XYZ refinement:
I 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.151011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.088764 restraints weight = 37333.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 3.19
r_work: 0.2882 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2901
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2901 r_free = 0.2901    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2901 r_free = 0.2901    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2901
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11794  Z= 0.119
  Angle     :  0.465   7.242  15926  Z= 0.246
  Chirality :  0.042   0.143   1801
  Planarity :  0.003   0.045   2049
  Dihedral  :  8.277 121.666   1675
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.10 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  1.62 (0.23), residues: 1451
  helix:  1.97 (0.19), residues: 799
  sheet:  0.44 (0.39), residues: 202
  loop : -0.18 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 108 
 HIS   0.009   0.001   HIS B  71 
 PHE   0.009   0.001   PHE H  93 
 TYR   0.013   0.002   TYR E  80 
 ARG   0.004   0.000   ARG H  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04530 (  641)
  hydrogen bonds       : angle       4.24609 ( 1871)
  covalent geometry    : bond        0.00268 (11792)
  covalent geometry    : angle       0.46503 (15926)
  Misc. bond           : bond        0.00039 (    2)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 142
  time to evaluate  : 1.376 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7996 (tm-30)
REVERT: A  226 LYS cc_start: 0.8486 (mtpt) cc_final: 0.7759 (mptp)
REVERT: A  347 LYS cc_start: 0.8285 (mttm) cc_final: 0.7858 (mtmt)
REVERT: A  417 GLU cc_start: 0.7754 (tt0) cc_final: 0.7143 (mp0)
REVERT: B   18 ARG cc_start: 0.7938 (mtt90) cc_final: 0.7606 (mtt90)
REVERT: B   41 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8262 (mtt90)
REVERT: D   89 ARG cc_start: 0.7654 (mmt90) cc_final: 0.6759 (mtp85)
REVERT: E  145 ARG cc_start: 0.7448 (mtm110) cc_final: 0.6667 (pmt170)
REVERT: E  247 MET cc_start: 0.8835 (mtt) cc_final: 0.8418 (mtt)
REVERT: E  275 ARG cc_start: 0.8030 (tpp-160) cc_final: 0.7522 (ttt-90)
REVERT: E  347 LYS cc_start: 0.7678 (mmtt) cc_final: 0.7440 (mmtt)
REVERT: E  417 GLU cc_start: 0.7801 (tt0) cc_final: 0.7037 (mp0)
REVERT: F   71 HIS cc_start: 0.7896 (t-90) cc_final: 0.7645 (t-90)
REVERT: H  118 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7259 (mm)
  outliers start: 28
  outliers final: 9
  residues processed: 158
  average time/residue: 1.5661
  time to fit residues: 264.3446
Evaluate side-chains
  145 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 133
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 GLU
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue   41 ARG
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain E residue  144 SER
Chi-restraints excluded: chain H residue   79 VAL
Chi-restraints excluded: chain H residue   86 VAL
Chi-restraints excluded: chain H residue  118 LEU
Chi-restraints excluded: chain H residue  136 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 131 optimal weight:    1.9990
   chunk 59 optimal weight:    9.9990
   chunk 66 optimal weight:    4.9990
   chunk 127 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 114 optimal weight:    0.7980
   chunk 134 optimal weight:    6.9990
   chunk 74 optimal weight:    4.9990
   chunk 124 optimal weight:    2.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
I 151 ASN
H  42 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.147943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.085227 restraints weight = 41938.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 3.31
r_work: 0.2791 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2834
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2834
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  11794  Z= 0.203
  Angle     :  0.552   7.716  15926  Z= 0.292
  Chirality :  0.046   0.153   1801
  Planarity :  0.004   0.045   2049
  Dihedral  :  8.398 121.123   1674
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.26 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  1.41 (0.22), residues: 1451
  helix:  1.81 (0.18), residues: 799
  sheet:  0.31 (0.39), residues: 203
  loop : -0.28 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 108 
 HIS   0.007   0.001   HIS B  71 
 PHE   0.011   0.002   PHE E 141 
 TYR   0.017   0.002   TYR A 260 
 ARG   0.004   0.000   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05741 (  641)
  hydrogen bonds       : angle       4.46568 ( 1871)
  covalent geometry    : bond        0.00495 (11792)
  covalent geometry    : angle       0.55181 (15926)
  Misc. bond           : bond        0.00065 (    2)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 141
  time to evaluate  : 1.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7871 (tm-30)
REVERT: A  145 ARG cc_start: 0.7677 (mtm110) cc_final: 0.7426 (mtp-110)
REVERT: A  226 LYS cc_start: 0.8409 (mtpt) cc_final: 0.7886 (mtmm)
REVERT: A  347 LYS cc_start: 0.8113 (mttm) cc_final: 0.7682 (mtmt)
REVERT: A  364 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7257 (tt0)
REVERT: A  417 GLU cc_start: 0.7792 (tt0) cc_final: 0.6908 (mp0)
REVERT: B   18 ARG cc_start: 0.7725 (mtt90) cc_final: 0.7394 (mtt90)
REVERT: B   41 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7626 (ttm170)
REVERT: B   51 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6756 (mm-30)
REVERT: D   89 ARG cc_start: 0.7496 (mmt90) cc_final: 0.6503 (mtp85)
REVERT: E  145 ARG cc_start: 0.7479 (mtm110) cc_final: 0.6577 (pmt170)
REVERT: E  247 MET cc_start: 0.8702 (mtt) cc_final: 0.8303 (mtt)
REVERT: E  275 ARG cc_start: 0.7945 (tpp-160) cc_final: 0.7441 (ttt-90)
REVERT: E  417 GLU cc_start: 0.7718 (tt0) cc_final: 0.6727 (mp0)
REVERT: F   21 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8238 (mttt)
REVERT: F   71 HIS cc_start: 0.7793 (t-90) cc_final: 0.7448 (t-90)
REVERT: H  118 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7222 (mm)
REVERT: H  129 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6619 (mp)
  outliers start: 31
  outliers final: 12
  residues processed: 164
  average time/residue: 1.5475
  time to fit residues: 271.2760
Evaluate side-chains
  159 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 GLU
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue   41 ARG
Chi-restraints excluded: chain B residue   51 GLU
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain E residue   61 MET
Chi-restraints excluded: chain E residue  144 SER
Chi-restraints excluded: chain E residue  400 ASP
Chi-restraints excluded: chain F residue   21 LYS
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   79 VAL
Chi-restraints excluded: chain H residue   86 VAL
Chi-restraints excluded: chain H residue  118 LEU
Chi-restraints excluded: chain H residue  129 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 126 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 100 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 65 optimal weight:    9.9990
   chunk 90 optimal weight:    0.7980
   chunk 129 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 92 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
I 151 ASN
E 429 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.150806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.088773 restraints weight = 34643.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 3.12
r_work: 0.2882 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2871
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2871
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11794  Z= 0.120
  Angle     :  0.465   6.910  15926  Z= 0.246
  Chirality :  0.042   0.144   1801
  Planarity :  0.003   0.043   2049
  Dihedral  :  7.343  86.399   1674
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 18.66 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  1.61 (0.23), residues: 1451
  helix:  1.99 (0.19), residues: 800
  sheet:  0.35 (0.39), residues: 201
  loop : -0.20 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H 108 
 HIS   0.006   0.001   HIS B  71 
 PHE   0.008   0.001   PHE E 141 
 TYR   0.014   0.002   TYR E  80 
 ARG   0.003   0.000   ARG H  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04545 (  641)
  hydrogen bonds       : angle       4.22964 ( 1871)
  covalent geometry    : bond        0.00271 (11792)
  covalent geometry    : angle       0.46542 (15926)
  Misc. bond           : bond        0.00028 (    2)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 1.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8036 (tm-30)
REVERT: A  226 LYS cc_start: 0.8535 (mtpt) cc_final: 0.8080 (mtmm)
REVERT: A  347 LYS cc_start: 0.8318 (mttm) cc_final: 0.7886 (mtmt)
REVERT: A  364 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7509 (tt0)
REVERT: A  417 GLU cc_start: 0.7826 (tt0) cc_final: 0.7199 (mp0)
REVERT: B   18 ARG cc_start: 0.7958 (mtt90) cc_final: 0.7648 (mtt90)
REVERT: B   41 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8270 (mtt90)
REVERT: D   89 ARG cc_start: 0.7652 (mmt90) cc_final: 0.6729 (mtp85)
REVERT: E  100 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7832 (tt0)
REVERT: E  145 ARG cc_start: 0.7570 (mtm110) cc_final: 0.6797 (pmt170)
REVERT: E  247 MET cc_start: 0.8854 (mtt) cc_final: 0.8449 (mtt)
REVERT: E  275 ARG cc_start: 0.8064 (tpp-160) cc_final: 0.7574 (tpt-90)
REVERT: E  417 GLU cc_start: 0.7869 (tt0) cc_final: 0.7069 (mp0)
REVERT: F   21 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8419 (mttt)
REVERT: F   71 HIS cc_start: 0.7912 (t-90) cc_final: 0.7685 (t-90)
REVERT: H  118 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7267 (mm)
  outliers start: 24
  outliers final: 13
  residues processed: 157
  average time/residue: 1.5391
  time to fit residues: 258.1759
Evaluate side-chains
  156 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 1.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 GLU
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue   41 ARG
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain E residue  100 GLU
Chi-restraints excluded: chain E residue  144 SER
Chi-restraints excluded: chain E residue  400 ASP
Chi-restraints excluded: chain F residue   21 LYS
Chi-restraints excluded: chain F residue   23 PHE
Chi-restraints excluded: chain H residue   41 ASP
Chi-restraints excluded: chain H residue   79 VAL
Chi-restraints excluded: chain H residue   86 VAL
Chi-restraints excluded: chain H residue  118 LEU
Chi-restraints excluded: chain H residue  136 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 101 optimal weight:    6.9990
   chunk 88 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 130 optimal weight:    0.0970
   chunk 103 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9990
   chunk 85 optimal weight:    0.7980
   chunk 100 optimal weight:    4.9990
   chunk 44 optimal weight:    7.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
I 151 ASN
E 331 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.150765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.088619 restraints weight = 36171.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 3.17
r_work: 0.2876 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2880
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2880
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11794  Z= 0.121
  Angle     :  0.467   8.364  15926  Z= 0.246
  Chirality :  0.042   0.143   1801
  Planarity :  0.003   0.043   2049
  Dihedral  :  6.700  80.194   1674
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.58 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  1.67 (0.23), residues: 1451
  helix:  2.02 (0.19), residues: 800
  sheet:  0.38 (0.39), residues: 201
  loop : -0.15 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H 108 
 HIS   0.005   0.001   HIS B  71 
 PHE   0.009   0.001   PHE H  93 
 TYR   0.013   0.002   TYR E  80 
 ARG   0.004   0.000   ARG H  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04563 (  641)
  hydrogen bonds       : angle       4.21079 ( 1871)
  covalent geometry    : bond        0.00276 (11792)
  covalent geometry    : angle       0.46655 (15926)
  Misc. bond           : bond        0.00032 (    2)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 1.289 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7998 (tm-30)
REVERT: A  145 ARG cc_start: 0.7685 (mtp-110) cc_final: 0.6417 (pmt170)
REVERT: A  226 LYS cc_start: 0.8519 (mtpt) cc_final: 0.8096 (mtmm)
REVERT: A  347 LYS cc_start: 0.8280 (mttm) cc_final: 0.7848 (mtmt)
REVERT: A  362 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.6536 (tm-30)
REVERT: A  364 GLU cc_start: 0.7785 (tm-30) cc_final: 0.6987 (tm-30)
REVERT: A  417 GLU cc_start: 0.7835 (tt0) cc_final: 0.7191 (mp0)
REVERT: B   18 ARG cc_start: 0.7958 (mtt90) cc_final: 0.7647 (mtt90)
REVERT: B   41 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8269 (mtt90)
REVERT: D   89 ARG cc_start: 0.7667 (mmt90) cc_final: 0.6741 (mtp85)
REVERT: E  100 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7839 (tt0)
REVERT: E  145 ARG cc_start: 0.7573 (mtm110) cc_final: 0.6814 (pmt170)
REVERT: E  247 MET cc_start: 0.8853 (mtt) cc_final: 0.8451 (mtt)
REVERT: E  275 ARG cc_start: 0.8054 (tpp-160) cc_final: 0.7579 (tpt-90)
REVERT: E  417 GLU cc_start: 0.7851 (tt0) cc_final: 0.7084 (mp0)
REVERT: F   21 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8424 (mttt)
REVERT: F   71 HIS cc_start: 0.7874 (t-90) cc_final: 0.7636 (t-90)
REVERT: H  118 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7230 (mm)
  outliers start: 28
  outliers final: 14
  residues processed: 153
  average time/residue: 1.5675
  time to fit residues: 256.7473
Evaluate side-chains
  155 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 GLU
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue   41 ARG
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain E residue   61 MET
Chi-restraints excluded: chain E residue  100 GLU
Chi-restraints excluded: chain E residue  144 SER
Chi-restraints excluded: chain E residue  400 ASP
Chi-restraints excluded: chain F residue   21 LYS
Chi-restraints excluded: chain F residue   23 PHE
Chi-restraints excluded: chain H residue   41 ASP
Chi-restraints excluded: chain H residue   79 VAL
Chi-restraints excluded: chain H residue   86 VAL
Chi-restraints excluded: chain H residue  118 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 133 optimal weight:    0.0470
   chunk 18 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 131 optimal weight:   10.0000
   chunk 123 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    0.8480

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

Flipped N/Q/H residues before XYZ refinement:
E 331 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.151798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.089561 restraints weight = 40183.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 3.30
r_work: 0.2891 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2881
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2881
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11794  Z= 0.105
  Angle     :  0.444   7.689  15926  Z= 0.235
  Chirality :  0.041   0.148   1801
  Planarity :  0.003   0.042   2049
  Dihedral  :  6.192  82.554   1674
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 19.14 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  1.74 (0.23), residues: 1451
  helix:  2.10 (0.19), residues: 799
  sheet:  0.42 (0.39), residues: 202
  loop : -0.16 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H 108 
 HIS   0.005   0.001   HIS B  71 
 PHE   0.009   0.001   PHE H  93 
 TYR   0.012   0.001   TYR E  80 
 ARG   0.004   0.000   ARG H  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04185 (  641)
  hydrogen bonds       : angle       4.12341 ( 1871)
  covalent geometry    : bond        0.00231 (11792)
  covalent geometry    : angle       0.44404 (15926)
  Misc. bond           : bond        0.00027 (    2)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 138
  time to evaluate  : 1.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7980 (tm-30)
REVERT: A  145 ARG cc_start: 0.7710 (mtp-110) cc_final: 0.6426 (pmt170)
REVERT: A  226 LYS cc_start: 0.8482 (mtpt) cc_final: 0.7798 (mptp)
REVERT: A  347 LYS cc_start: 0.8291 (mttm) cc_final: 0.7832 (mtmt)
REVERT: A  364 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7264 (tm-30)
REVERT: A  417 GLU cc_start: 0.7847 (tt0) cc_final: 0.7195 (mp0)
REVERT: B   18 ARG cc_start: 0.7972 (mtt90) cc_final: 0.7659 (mtt90)
REVERT: B   41 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8260 (mtt90)
REVERT: B   51 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6457 (tp30)
REVERT: D   89 ARG cc_start: 0.7669 (mmt90) cc_final: 0.6726 (mtp85)
REVERT: E  100 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7823 (tt0)
REVERT: E  145 ARG cc_start: 0.7566 (mtm110) cc_final: 0.6822 (pmt170)
REVERT: E  247 MET cc_start: 0.8869 (mtt) cc_final: 0.8460 (mtt)
REVERT: E  417 GLU cc_start: 0.7865 (tt0) cc_final: 0.7126 (mp0)
REVERT: F   42 GLU cc_start: 0.7780 (tt0) cc_final: 0.7153 (pt0)
REVERT: F   71 HIS cc_start: 0.7844 (t-90) cc_final: 0.7601 (t-90)
REVERT: H  118 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7182 (mm)
  outliers start: 25
  outliers final: 11
  residues processed: 154
  average time/residue: 1.6391
  time to fit residues: 269.9655
Evaluate side-chains
  148 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 1.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 GLU
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue   41 ARG
Chi-restraints excluded: chain B residue   51 GLU
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain E residue   61 MET
Chi-restraints excluded: chain E residue  100 GLU
Chi-restraints excluded: chain E residue  144 SER
Chi-restraints excluded: chain E residue  400 ASP
Chi-restraints excluded: chain F residue   23 PHE
Chi-restraints excluded: chain H residue   79 VAL
Chi-restraints excluded: chain H residue   86 VAL
Chi-restraints excluded: chain H residue  118 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 110 optimal weight:   10.0000
   chunk 129 optimal weight:    5.9990
   chunk 118 optimal weight:    3.9990
   chunk 112 optimal weight:    3.9990
   chunk 72 optimal weight:   10.0000
   chunk 102 optimal weight:    0.6980
   chunk 121 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 122 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   overall best weight:    1.4782

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

Flipped N/Q/H residues before XYZ refinement:
I 151 ASN
E 331 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.150120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.087795 restraints weight = 38274.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 3.19
r_work: 0.2867 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2878
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2878
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11794  Z= 0.137
  Angle     :  0.481   7.576  15926  Z= 0.254
  Chirality :  0.043   0.145   1801
  Planarity :  0.004   0.042   2049
  Dihedral  :  6.081  78.252   1673
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.66 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  1.67 (0.23), residues: 1451
  helix:  2.03 (0.19), residues: 800
  sheet:  0.36 (0.39), residues: 201
  loop : -0.16 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H 108 
 HIS   0.005   0.001   HIS B  71 
 PHE   0.009   0.001   PHE H  93 
 TYR   0.014   0.002   TYR E  80 
 ARG   0.004   0.000   ARG H  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04778 (  641)
  hydrogen bonds       : angle       4.22993 ( 1871)
  covalent geometry    : bond        0.00322 (11792)
  covalent geometry    : angle       0.48079 (15926)
  Misc. bond           : bond        0.00048 (    2)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 3.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7775 (tm-30)
REVERT: A  145 ARG cc_start: 0.7531 (mtp-110) cc_final: 0.6176 (pmt170)
REVERT: A  226 LYS cc_start: 0.8378 (mtpt) cc_final: 0.7883 (mtmm)
REVERT: A  347 LYS cc_start: 0.8099 (mttm) cc_final: 0.7639 (mtmt)
REVERT: A  364 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7075 (tm-30)
REVERT: A  417 GLU cc_start: 0.7702 (tt0) cc_final: 0.6920 (mp0)
REVERT: B   18 ARG cc_start: 0.7679 (mtt90) cc_final: 0.7340 (mtt90)
REVERT: B   41 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8065 (mtt90)
REVERT: B   51 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6676 (mm-30)
REVERT: D   89 ARG cc_start: 0.7462 (mmt90) cc_final: 0.6491 (mtp85)
REVERT: I  189 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6854 (mt-10)
REVERT: E  100 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7582 (tt0)
REVERT: E  145 ARG cc_start: 0.7438 (mtm110) cc_final: 0.6599 (pmt170)
REVERT: E  247 MET cc_start: 0.8718 (mtt) cc_final: 0.8308 (mtt)
REVERT: E  291 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7806 (mtt)
REVERT: E  417 GLU cc_start: 0.7688 (tt0) cc_final: 0.6801 (mp0)
REVERT: F   71 HIS cc_start: 0.7593 (t-90) cc_final: 0.7272 (t-90)
REVERT: H  118 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7157 (mm)
  outliers start: 25
  outliers final: 13
  residues processed: 148
  average time/residue: 2.1160
  time to fit residues: 335.8952
Evaluate side-chains
  155 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 2.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 GLU
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue   41 ARG
Chi-restraints excluded: chain B residue   51 GLU
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain I residue  189 GLU
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain E residue   61 MET
Chi-restraints excluded: chain E residue  100 GLU
Chi-restraints excluded: chain E residue  144 SER
Chi-restraints excluded: chain E residue  291 MET
Chi-restraints excluded: chain E residue  400 ASP
Chi-restraints excluded: chain F residue   23 PHE
Chi-restraints excluded: chain H residue   79 VAL
Chi-restraints excluded: chain H residue   86 VAL
Chi-restraints excluded: chain H residue  118 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 61 optimal weight:    9.9990
   chunk 109 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 52 optimal weight:   10.0000
   chunk 6 optimal weight:    0.7980
   chunk 113 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
I 151 ASN
E 331 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.151683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.089728 restraints weight = 44311.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 3.69
r_work: 0.2872 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11794  Z= 0.109
  Angle     :  0.451   7.300  15926  Z= 0.238
  Chirality :  0.041   0.142   1801
  Planarity :  0.003   0.042   2049
  Dihedral  :  5.785  81.586   1673
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 19.38 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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 (0.23), residues: 1451
  helix:  2.10 (0.19), residues: 799
  sheet:  0.42 (0.39), residues: 202
  loop : -0.13 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP I 168 
 HIS   0.005   0.001   HIS B  71 
 PHE   0.009   0.001   PHE H  93 
 TYR   0.013   0.001   TYR E  80 
 ARG   0.004   0.000   ARG H  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04281 (  641)
  hydrogen bonds       : angle       4.14279 ( 1871)
  covalent geometry    : bond        0.00242 (11792)
  covalent geometry    : angle       0.45132 (15926)
  Misc. bond           : bond        0.00028 (    2)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 1.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7995 (tm-30)
REVERT: A  145 ARG cc_start: 0.7676 (mtp-110) cc_final: 0.6364 (pmt170)
REVERT: A  226 LYS cc_start: 0.8520 (mtpt) cc_final: 0.7804 (mptp)
REVERT: A  347 LYS cc_start: 0.8265 (mttm) cc_final: 0.7809 (mtmt)
REVERT: A  364 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7308 (tm-30)
REVERT: A  417 GLU cc_start: 0.7868 (tt0) cc_final: 0.7175 (mp0)
REVERT: B   18 ARG cc_start: 0.7957 (mtt90) cc_final: 0.7649 (mtt90)
REVERT: B   41 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8247 (mtt90)
REVERT: B   51 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6447 (tp30)
REVERT: D   89 ARG cc_start: 0.7629 (mmt90) cc_final: 0.6676 (mtp85)
REVERT: E  100 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7844 (tt0)
REVERT: E  145 ARG cc_start: 0.7585 (mtm110) cc_final: 0.6796 (pmt170)
REVERT: E  247 MET cc_start: 0.8860 (mtt) cc_final: 0.8449 (mtt)
REVERT: E  273 ARG cc_start: 0.8101 (ttt-90) cc_final: 0.7481 (ttt90)
REVERT: E  417 GLU cc_start: 0.7883 (tt0) cc_final: 0.7092 (mp0)
REVERT: F   42 GLU cc_start: 0.7796 (tt0) cc_final: 0.7158 (pt0)
REVERT: F   71 HIS cc_start: 0.7852 (t-90) cc_final: 0.7600 (t-90)
REVERT: H  118 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7166 (mm)
  outliers start: 21
  outliers final: 13
  residues processed: 150
  average time/residue: 1.5610
  time to fit residues: 250.4875
Evaluate side-chains
  155 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 1.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 GLU
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue   41 ARG
Chi-restraints excluded: chain B residue   51 GLU
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain E residue   61 MET
Chi-restraints excluded: chain E residue  100 GLU
Chi-restraints excluded: chain E residue  144 SER
Chi-restraints excluded: chain E residue  400 ASP
Chi-restraints excluded: chain F residue   23 PHE
Chi-restraints excluded: chain H residue   79 VAL
Chi-restraints excluded: chain H residue   86 VAL
Chi-restraints excluded: chain H residue  118 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 91 optimal weight:    5.9990
   chunk 93 optimal weight:    1.9990
   chunk 135 optimal weight:    6.9990
   chunk 142 optimal weight:    0.4980
   chunk 42 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 63 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 101 optimal weight:    0.5980
   chunk 75 optimal weight:    5.9990
   chunk 61 optimal weight:    9.9990
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
I 151 ASN
E 331 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.149088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.085869 restraints weight = 36568.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 3.25
r_work: 0.2847 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2847
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2847
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  11794  Z= 0.216
  Angle     :  0.566   9.188  15926  Z= 0.297
  Chirality :  0.046   0.155   1801
  Planarity :  0.004   0.043   2049
  Dihedral  :  6.680  70.501   1673
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 19.06 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  1.44 (0.22), residues: 1451
  helix:  1.84 (0.18), residues: 798
  sheet:  0.32 (0.39), residues: 202
  loop : -0.28 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP I 168 
 HIS   0.004   0.001   HIS E 319 
 PHE   0.010   0.002   PHE E 141 
 TYR   0.017   0.003   TYR E  80 
 ARG   0.004   0.001   ARG E 292 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05772 (  641)
  hydrogen bonds       : angle       4.43851 ( 1871)
  covalent geometry    : bond        0.00532 (11792)
  covalent geometry    : angle       0.56567 (15926)
  Misc. bond           : bond        0.00076 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12187.55 seconds
wall clock time: 217 minutes 41.02 seconds (13061.02 seconds total)