Starting phenix.real_space_refine
on Thu Jul  2 08:47:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uin_64198/07_2026/9uin_64198.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uin_64198/07_2026/9uin_64198.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uin_64198/07_2026/9uin_64198.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uin_64198/07_2026/9uin_64198.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uin_64198/07_2026/9uin_64198.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uin_64198/07_2026/9uin_64198.map"
  }
  resolution = 3.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.039
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
     Cu      6      5.60       5
     P      10      5.49       5
     S      38      5.16       5
     C    4854      2.51       5
     N    1308      2.21       5
     O    1474      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7690
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 3741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 484, 3741
          Classifications: {'peptide': 484}
          Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 464}
    Chain: "A"
      Number of atoms: 3741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 484, 3741
          Classifications: {'peptide': 484}
          Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 464}
    Chain: "B"
      Number of atoms: 104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 101
          Ad-hoc single atom residues: {' CU': 3}
          Unusual residues: {'FAD': 1, 'TXP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 101
          Ad-hoc single atom residues: {' CU': 3}
          Unusual residues: {'FAD': 1, 'TXP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Chain breaks: 3

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    359  SG  CYS B  59      34.739  33.083  38.357  1.00 55.17           S
  ATOM    391  SG  CYS B  64      34.309  36.550  37.870  1.00 52.37           S
  ATOM   4100  SG  CYS A  59      67.263  58.717  38.361  1.00 55.17           S
  ATOM   4132  SG  CYS A  64      67.693  55.250  37.874  1.00 52.37           S

  Time building chain proxies: 1.51, per 1000 atoms: 0.20
  Number of scatterers: 7690
  At special positions: 0
  Unit cell: (102.85, 92.65, 74.8, 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)
     Cu      6     28.99
     S      38     16.00
     P      10     15.00
     O    1474      8.00
     N    1308      7.00
     C    4854      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=0, symmetry=0
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 391.8 milliseconds
  

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1740

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      35.8% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'B' and resid 21 through 33
      removed outlier: 3.578A  pdb=" N   LEU B  25 " --> pdb=" O   GLY B  21 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLN B  33 " --> pdb=" O   LYS B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 62
      removed outlier: 3.819A  pdb=" N   ASN B  61 " --> pdb=" O   GLY B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 83
      removed outlier: 3.857A  pdb=" N   GLN B  81 " --> pdb=" O   GLY B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 87
      removed outlier: 3.552A  pdb=" N   GLY B  87 " --> pdb=" O   ARG B  84 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 84 through 87'
    Processing helix  chain 'B' and resid 97 through 123
      removed outlier: 3.678A  pdb=" N   MET B 101 " --> pdb=" O   ASP B  97 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ARG B 121 " --> pdb=" O   ARG B 117 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LYS B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 184
      removed outlier: 3.628A  pdb=" N   LEU B 183 " --> pdb=" O   SER B 179 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   PHE B 184 " --> pdb=" O   SER B 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 179 through 184'
    Processing helix  chain 'B' and resid 199 through 211
    Processing helix  chain 'B' and resid 229 through 244
    Processing helix  chain 'B' and resid 301 through 306
      removed outlier: 4.367A  pdb=" N   VAL B 305 " --> pdb=" O   GLY B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 359
      removed outlier: 3.614A  pdb=" N   ALA B 346 " --> pdb=" O   LEU B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 395
    Processing helix  chain 'B' and resid 409 through 413
      removed outlier: 3.687A  pdb=" N   ILE B 413 " --> pdb=" O   GLU B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 456
      removed outlier: 3.567A  pdb=" N   VAL B 448 " --> pdb=" O   ASN B 444 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLY B 451 " --> pdb=" O   GLU B 447 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE B 452 " --> pdb=" O   VAL B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 468
    Processing helix  chain 'B' and resid 475 through 482
      removed outlier: 3.516A  pdb=" N   VAL B 478 " --> pdb=" O   CYS B 475 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   LEU B 482 " --> pdb=" O   PHE B 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 33
      removed outlier: 3.578A  pdb=" N   LEU A  25 " --> pdb=" O   GLY A  21 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLN A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 62
      removed outlier: 3.819A  pdb=" N   ASN A  61 " --> pdb=" O   GLY A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 83
      removed outlier: 3.858A  pdb=" N   GLN A  81 " --> pdb=" O   GLY A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 87
      removed outlier: 3.552A  pdb=" N   GLY A  87 " --> pdb=" O   ARG A  84 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 84 through 87'
    Processing helix  chain 'A' and resid 97 through 123
      removed outlier: 3.678A  pdb=" N   MET A 101 " --> pdb=" O   ASP A  97 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ARG A 121 " --> pdb=" O   ARG A 117 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LYS A 123 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 184
      removed outlier: 3.628A  pdb=" N   LEU A 183 " --> pdb=" O   SER A 179 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   PHE A 184 " --> pdb=" O   SER A 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 179 through 184'
    Processing helix  chain 'A' and resid 199 through 211
    Processing helix  chain 'A' and resid 229 through 244
    Processing helix  chain 'A' and resid 301 through 306
      removed outlier: 4.366A  pdb=" N   VAL A 305 " --> pdb=" O   GLY A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 359
      removed outlier: 3.614A  pdb=" N   ALA A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 395
    Processing helix  chain 'A' and resid 408 through 413
      removed outlier: 3.575A  pdb=" N   THR A 412 " --> pdb=" O   PRO A 408 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ILE A 413 " --> pdb=" O   LEU A 409 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 408 through 413'
    Processing helix  chain 'A' and resid 444 through 456
      removed outlier: 3.567A  pdb=" N   VAL A 448 " --> pdb=" O   ASN A 444 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   GLY A 451 " --> pdb=" O   GLU A 447 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE A 452 " --> pdb=" O   VAL A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 468
    Processing helix  chain 'A' and resid 475 through 482
      removed outlier: 3.516A  pdb=" N   VAL A 478 " --> pdb=" O   CYS A 475 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   LEU A 482 " --> pdb=" O   PHE A 479 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 126 through 128
      removed outlier: 6.123A  pdb=" N   VAL B  40 " --> pdb=" O   GLU B 128 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ILE B  16 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 134 through 136
      removed outlier: 4.254A  pdb=" N   GLY B 136 " --> pdb=" O   ARG B 139 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 163 through 165
    Processing sheet with id=AA4, first strand: chain 'B' and resid 246 through 249
      removed outlier: 3.673A  pdb=" N   LYS B 246 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   LEU B 194 " --> pdb=" O   MET B 288 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 260
      removed outlier: 6.524A  pdb=" N   VAL B 270 " --> pdb=" O   ILE B 254 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   VAL B 256 " --> pdb=" O   ARG B 268 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ARG B 268 " --> pdb=" O   VAL B 256 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   GLN B 258 " --> pdb=" O   ARG B 266 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   ARG B 266 " --> pdb=" O   GLN B 258 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 372 through 374
      removed outlier: 6.583A  pdb=" N   ILE B 426 " --> pdb=" O   VAL B 436 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   PHE B 438 " --> pdb=" O   LYS B 424 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   LYS B 424 " --> pdb=" O   PHE B 438 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   VAL B 440 " --> pdb=" O   TYR B 422 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   TYR B 422 " --> pdb=" O   VAL B 440 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   CYS B 421 " --> pdb=" O   PHE B 406 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 126 through 128
      removed outlier: 6.123A  pdb=" N   VAL A  40 " --> pdb=" O   GLU A 128 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ILE A  16 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 134 through 136
      removed outlier: 4.254A  pdb=" N   GLY A 136 " --> pdb=" O   ARG A 139 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 163 through 165
    Processing sheet with id=AB1, first strand: chain 'A' and resid 246 through 249
      removed outlier: 3.674A  pdb=" N   LYS A 246 " --> pdb=" O   VAL A 216 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   LEU A 194 " --> pdb=" O   MET A 288 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 251 through 260
      removed outlier: 6.523A  pdb=" N   VAL A 270 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   VAL A 256 " --> pdb=" O   ARG A 268 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ARG A 268 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 4.936A  pdb=" N   GLN A 258 " --> pdb=" O   ARG A 266 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   ARG A 266 " --> pdb=" O   GLN A 258 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 372 through 374
      removed outlier: 6.583A  pdb=" N   ILE A 426 " --> pdb=" O   VAL A 436 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   PHE A 438 " --> pdb=" O   LYS A 424 " (cutoff:3.500A)
      removed outlier: 7.267A  pdb=" N   LYS A 424 " --> pdb=" O   PHE A 438 " (cutoff:3.500A)
      removed outlier: 4.971A  pdb=" N   VAL A 440 " --> pdb=" O   TYR A 422 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   TYR A 422 " --> pdb=" O   VAL A 440 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   CYS A 421 " --> pdb=" O   PHE A 406 " (cutoff:3.500A)

    273 hydrogen bonds defined for protein.
    768 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: 0.97

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1288
        1.31 -     1.43: 2021
        1.43 -     1.56: 4467
        1.56 -     1.68: 22
        1.68 -     1.81: 52
  Bond restraints: 7850
  Sorted by residual:
  bond pdb=" C3' TXP B 501 "
       pdb=" C4' TXP B 501 "
    ideal  model  delta    sigma   weight residual
    1.544  1.294  0.250 2.00e-02 2.50e+03 1.56e+02
  bond pdb=" C3' TXP A 501 "
       pdb=" C4' TXP A 501 "
    ideal  model  delta    sigma   weight residual
    1.544  1.295  0.249 2.00e-02 2.50e+03 1.55e+02
  bond pdb="C1'A TXP A 501 "
       pdb="C2'A TXP A 501 "
    ideal  model  delta    sigma   weight residual
    1.526  1.300  0.226 2.00e-02 2.50e+03 1.28e+02
  bond pdb="C1'A TXP B 501 "
       pdb="C2'A TXP B 501 "
    ideal  model  delta    sigma   weight residual
    1.526  1.300  0.226 2.00e-02 2.50e+03 1.27e+02
  bond pdb=" C1' TXP B 501 "
       pdb=" C2' TXP B 501 "
    ideal  model  delta    sigma   weight residual
    1.530  1.328  0.202 2.00e-02 2.50e+03 1.02e+02
  ... (remaining 7845 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.87: 10436
        2.87 -     5.73: 183
        5.73 -     8.60: 31
        8.60 -    11.47: 14
       11.47 -    14.34: 6
  Bond angle restraints: 10670
  Sorted by residual:
  angle pdb=" N   THR A 412 "
        pdb=" CA  THR A 412 "
        pdb=" C   THR A 412 "
      ideal   model   delta    sigma   weight residual
     111.28  116.95   -5.67 1.09e+00 8.42e-01 2.71e+01
  angle pdb=" N   VAL B 220 "
        pdb=" CA  VAL B 220 "
        pdb=" C   VAL B 220 "
      ideal   model   delta    sigma   weight residual
     107.80  114.94   -7.14 1.45e+00 4.76e-01 2.42e+01
  angle pdb=" O1P FAD A 502 "
        pdb=" P   FAD A 502 "
        pdb=" O2P FAD A 502 "
      ideal   model   delta    sigma   weight residual
     122.50  108.16   14.34 3.00e+00 1.11e-01 2.28e+01
  angle pdb=" O1P FAD B 502 "
        pdb=" P   FAD B 502 "
        pdb=" O2P FAD B 502 "
      ideal   model   delta    sigma   weight residual
     122.50  108.16   14.34 3.00e+00 1.11e-01 2.28e+01
  angle pdb=" N   GLY B  56 "
        pdb=" CA  GLY B  56 "
        pdb=" C   GLY B  56 "
      ideal   model   delta    sigma   weight residual
     111.09  105.20    5.89 1.33e+00 5.65e-01 1.96e+01
  ... (remaining 10665 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.79: 4518
       34.79 -    69.58: 234
       69.58 -   104.37: 42
      104.37 -   139.17: 4
      139.17 -   173.96: 2
  Dihedral angle restraints: 4800
    sinusoidal: 2052
      harmonic: 2748
  Sorted by residual:
  dihedral pdb=" O3  TXP B 501 "
           pdb=" PN  TXP B 501 "
           pdb="O5'A TXP B 501 "
           pdb="C5'A TXP B 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -146.00   27.96 -173.96     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" O3  TXP A 501 "
           pdb=" PN  TXP A 501 "
           pdb="O5'A TXP A 501 "
           pdb="C5'A TXP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -146.00   20.76 -166.76     1      3.00e+01 1.11e-03 2.10e+01
  dihedral pdb=" C3N TXP A 501 "
           pdb=" C2N TXP A 501 "
           pdb=" N1N TXP A 501 "
           pdb=" C6N TXP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -67.86   59.04 -126.90     1      3.00e+01 1.11e-03 1.71e+01
  ... (remaining 4797 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.064: 1188
       1.064 -    2.128: 0
       2.128 -    3.192: 0
       3.192 -    4.256: 0
       4.256 -    5.320: 2
  Chirality restraints: 1190
  Sorted by residual:
  chirality pdb=" C3N TXP B 501 "
            pdb=" C2N TXP B 501 "
            pdb=" C4N TXP B 501 "
            pdb=" C7N TXP B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.65    2.67   -5.32 2.00e-01 2.50e+01 7.08e+02
  chirality pdb=" C3N TXP A 501 "
            pdb=" C2N TXP A 501 "
            pdb=" C4N TXP A 501 "
            pdb=" C7N TXP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.65    2.67   -5.32 2.00e-01 2.50e+01 7.06e+02
  chirality pdb=" CA  THR A 412 "
            pdb=" N   THR A 412 "
            pdb=" C   THR A 412 "
            pdb=" CB  THR A 412 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.32    0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 1187 not shown)

  Planarity restraints: 1338
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 220 "    0.011 2.00e-02 2.50e+03   2.23e-02 4.99e+00
        pdb=" C   VAL A 220 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   VAL A 220 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ARG A 221 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 200 "    0.026 2.00e-02 2.50e+03   1.52e-02 4.59e+00
        pdb=" CG  TYR A 200 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 200 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 200 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 200 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 200 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 200 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 200 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 200 "   -0.025 2.00e-02 2.50e+03   1.49e-02 4.47e+00
        pdb=" CG  TYR B 200 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 200 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 200 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 200 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 200 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 200 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B 200 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1335 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 763
        2.73 -     3.27: 6771
        3.27 -     3.81: 11417
        3.81 -     4.36: 14516
        4.36 -     4.90: 26021
  Nonbonded interactions: 59488
  Sorted by model distance:
  nonbonded pdb=" O   SER A 185 "
            pdb=" OG  SER A 185 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" O   SER B 185 "
            pdb=" OG  SER B 185 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" SG  CYS B  59 "
            pdb="CU    CU B 503 "
     model   vdw
     2.206 3.340
  nonbonded pdb=" SG  CYS A  59 "
            pdb="CU    CU A 503 "
     model   vdw
     2.206 3.340
  nonbonded pdb=" OG  SER B 276 "
            pdb=" N   GLU B 277 "
     model   vdw
     2.210 3.120
  ... (remaining 59483 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.380
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.250
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
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      :  0.015   0.250   7850  Z= 0.666
  Angle     :  1.102  14.337  10670  Z= 0.574
  Chirality :  0.225   5.320   1190
  Planarity :  0.005   0.044   1338
  Dihedral  : 20.788 173.958   3060
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.57 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 12.81 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.83 (0.23), residues: 964
  helix: -0.84 (0.26), residues: 276
  sheet: -1.83 (0.32), residues: 238
  loop : -2.55 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  52 
 TYR   0.033   0.003   TYR A 200 
 PHE   0.034   0.004   PHE A 208 
 TRP   0.012   0.002   TRP A 407 
 HIS   0.005   0.002   HIS B  96 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01466 /  0.67 ( 7850)
  covalent geometry    : angle       1.10237 /  0.57 (10670)
  hydrogen bonds       : bond        0.17320 / 11.36 (  273)
  hydrogen bonds       : angle       6.33693 /  4.29 (  768)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 78
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6613 (tm-30)
REVERT: B  334 ASP cc_start: 0.8527 (m-30) cc_final: 0.8250 (m-30)
REVERT: A  128 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6618 (tm-30)
REVERT: A  334 ASP cc_start: 0.8524 (m-30) cc_final: 0.8259 (m-30)
  outliers start: 49
  outliers final: 40
  residues processed: 122
  average time/residue: 0.0798
  time to fit residues: 12.6896
Evaluate side-chains
  108 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 66
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   64 CYS
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  182 ASP
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  320 ASP
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain B residue  435 VAL
Chi-restraints excluded: chain B residue  485 THR
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   64 CYS
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  182 ASP
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  250 GLN
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  386 SER
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  493 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0670
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.6318

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 ASN
B 369 ASN
B 419 ASN
B 428 ASN
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 234 ASN
A 369 ASN
A 419 ASN
A 428 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.145857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.117833 restraints weight = 8821.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.16
r_work: 0.3247 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.1292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7850  Z= 0.106
  Angle     :  0.534   9.893  10670  Z= 0.274
  Chirality :  0.045   0.145   1190
  Planarity :  0.004   0.035   1338
  Dihedral  : 16.633 171.163   1366
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 16.21 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.42 (0.25), residues: 964
  helix:  1.12 (0.29), residues: 268
  sheet: -1.05 (0.34), residues: 228
  loop : -2.17 (0.25), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 139 
 TYR   0.024   0.001   TYR A 200 
 PHE   0.018   0.001   PHE A 208 
 TRP   0.009   0.001   TRP A  98 
 HIS   0.001   0.000   HIS B 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00228 /  0.11 ( 7850)
  covalent geometry    : angle       0.53437 /  0.27 (10670)
  hydrogen bonds       : bond        0.04284 /  2.80 (  273)
  hydrogen bonds       : angle       4.55256 /  3.10 (  768)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 78
  time to evaluate  : 0.287 
Fit side-chains
REVERT: B  116 TYR cc_start: 0.7749 (m-80) cc_final: 0.7515 (m-80)
REVERT: B  128 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7196 (tm-30)
REVERT: B  152 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.7191 (p90)
REVERT: B  337 GLU cc_start: 0.8083 (tt0) cc_final: 0.7855 (tt0)
REVERT: A  128 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7190 (tm-30)
REVERT: A  152 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.7148 (p90)
REVERT: A  337 GLU cc_start: 0.8077 (tt0) cc_final: 0.7846 (tt0)
  outliers start: 33
  outliers final: 20
  residues processed: 108
  average time/residue: 0.0773
  time to fit residues: 11.5604
Evaluate side-chains
  87 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 63
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   64 CYS
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  152 TYR
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain A residue   64 CYS
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  250 GLN
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  493 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 67 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 48 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 42 optimal weight:    8.9990
   chunk 65 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  61 ASN
A  61 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.145066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.118460 restraints weight = 8760.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 2.05
r_work: 0.3243 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8693
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7850  Z= 0.122
  Angle     :  0.523   9.534  10670  Z= 0.264
  Chirality :  0.045   0.135   1190
  Planarity :  0.004   0.040   1338
  Dihedral  : 14.674 167.882   1326
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 16.21 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.26), residues: 964
  helix:  1.68 (0.30), residues: 268
  sheet: -0.73 (0.35), residues: 230
  loop : -1.85 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 139 
 TYR   0.024   0.001   TYR B 200 
 PHE   0.018   0.002   PHE A 208 
 TRP   0.007   0.001   TRP A 407 
 HIS   0.002   0.001   HIS B 138 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.12 ( 7850)
  covalent geometry    : angle       0.52308 /  0.26 (10670)
  hydrogen bonds       : bond        0.04422 /  2.86 (  273)
  hydrogen bonds       : angle       4.31668 /  2.96 (  768)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 69
  time to evaluate  : 0.313 
Fit side-chains
REVERT: B   29 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7811 (mttp)
REVERT: B  116 TYR cc_start: 0.7634 (m-80) cc_final: 0.7108 (m-80)
REVERT: B  152 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.7307 (p90)
REVERT: B  394 PHE cc_start: 0.7962 (m-80) cc_final: 0.7700 (m-80)
REVERT: A   29 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7820 (mttp)
REVERT: A  116 TYR cc_start: 0.7707 (m-80) cc_final: 0.7152 (m-80)
REVERT: A  152 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.7254 (p90)
REVERT: A  394 PHE cc_start: 0.7965 (m-80) cc_final: 0.7701 (m-80)
  outliers start: 36
  outliers final: 28
  residues processed: 99
  average time/residue: 0.0718
  time to fit residues: 9.7547
Evaluate side-chains
  92 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 60
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 LYS
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   64 CYS
Chi-restraints excluded: chain B residue  152 TYR
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   64 CYS
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  493 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 89 optimal weight:    5.9990
   chunk 70 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 1 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 59 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 94 optimal weight:    6.9990
   overall best weight:    0.9182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.144549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.117047 restraints weight = 8622.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 2.12
r_work: 0.3234 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7850  Z= 0.111
  Angle     :  0.503   9.904  10670  Z= 0.253
  Chirality :  0.044   0.146   1190
  Planarity :  0.004   0.041   1338
  Dihedral  : 12.394 118.177   1312
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 16.96 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.26), residues: 964
  helix:  1.57 (0.30), residues: 282
  sheet: -0.47 (0.35), residues: 230
  loop : -1.83 (0.26), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 139 
 TYR   0.023   0.001   TYR A 200 
 PHE   0.015   0.001   PHE A 208 
 TRP   0.006   0.001   TRP A  88 
 HIS   0.001   0.001   HIS B 138 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.11 ( 7850)
  covalent geometry    : angle       0.50319 /  0.25 (10670)
  hydrogen bonds       : bond        0.04031 /  2.61 (  273)
  hydrogen bonds       : angle       4.16078 /  2.86 (  768)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 71
  time to evaluate  : 0.235 
Fit side-chains
REVERT: B  116 TYR cc_start: 0.7570 (m-80) cc_final: 0.7052 (m-80)
REVERT: B  348 GLN cc_start: 0.7387 (tt0) cc_final: 0.7131 (mt0)
REVERT: A  116 TYR cc_start: 0.7585 (m-80) cc_final: 0.7113 (m-80)
REVERT: A  152 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.7268 (p90)
REVERT: A  348 GLN cc_start: 0.7363 (tt0) cc_final: 0.7106 (mt0)
  outliers start: 34
  outliers final: 29
  residues processed: 99
  average time/residue: 0.0692
  time to fit residues: 9.8326
Evaluate side-chains
  91 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 61
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   64 CYS
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   64 CYS
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  493 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.2980
   chunk 62 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 26 optimal weight:    7.9990
   chunk 76 optimal weight:    0.2980
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.6782

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.145917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.118319 restraints weight = 8511.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.11
r_work: 0.3254 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7850  Z= 0.094
  Angle     :  0.478  10.237  10670  Z= 0.239
  Chirality :  0.044   0.148   1190
  Planarity :  0.004   0.046   1338
  Dihedral  : 11.613 109.296   1312
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 16.08 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.27), residues: 964
  helix:  1.78 (0.30), residues: 284
  sheet: -0.22 (0.36), residues: 230
  loop : -1.60 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 139 
 TYR   0.022   0.001   TYR A 200 
 PHE   0.012   0.001   PHE B 208 
 TRP   0.007   0.001   TRP B  98 
 HIS   0.001   0.000   HIS A 138 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00214 /  0.09 ( 7850)
  covalent geometry    : angle       0.47839 /  0.24 (10670)
  hydrogen bonds       : bond        0.03577 /  2.33 (  273)
  hydrogen bonds       : angle       4.05016 /  2.79 (  768)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 69
  time to evaluate  : 0.297 
Fit side-chains
REVERT: B   29 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7791 (mttp)
REVERT: B  116 TYR cc_start: 0.7572 (m-80) cc_final: 0.7113 (m-80)
REVERT: B  348 GLN cc_start: 0.7403 (tt0) cc_final: 0.7154 (mt0)
REVERT: A  116 TYR cc_start: 0.7613 (m-80) cc_final: 0.7206 (m-80)
REVERT: A  348 GLN cc_start: 0.7378 (tt0) cc_final: 0.7127 (mt0)
  outliers start: 45
  outliers final: 33
  residues processed: 105
  average time/residue: 0.0707
  time to fit residues: 10.7964
Evaluate side-chains
  98 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 64
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 LYS
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  250 GLN
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  410 GLU
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  493 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 47 optimal weight:    0.3980
   chunk 82 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 35 optimal weight:    6.9990
   chunk 75 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0870
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.5758

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.147368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.119822 restraints weight = 8451.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 2.10
r_work: 0.3270 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7850  Z= 0.087
  Angle     :  0.465  10.078  10670  Z= 0.232
  Chirality :  0.043   0.145   1190
  Planarity :  0.004   0.046   1338
  Dihedral  : 10.983 108.101   1310
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 17.21 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.27), residues: 964
  helix:  1.94 (0.31), residues: 284
  sheet: -0.06 (0.36), residues: 230
  loop : -1.49 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 139 
 TYR   0.021   0.001   TYR A 200 
 PHE   0.010   0.001   PHE B 208 
 TRP   0.007   0.001   TRP B  98 
 HIS   0.001   0.000   HIS A 138 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00196 /  0.09 ( 7850)
  covalent geometry    : angle       0.46470 /  0.23 (10670)
  hydrogen bonds       : bond        0.03367 /  2.19 (  273)
  hydrogen bonds       : angle       3.96489 /  2.73 (  768)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 64
  time to evaluate  : 0.284 
Fit side-chains
REVERT: B  116 TYR cc_start: 0.7561 (m-80) cc_final: 0.7138 (m-80)
REVERT: B  394 PHE cc_start: 0.7963 (m-80) cc_final: 0.7730 (m-80)
REVERT: A  116 TYR cc_start: 0.7594 (m-80) cc_final: 0.7238 (m-80)
REVERT: A  394 PHE cc_start: 0.7971 (m-80) cc_final: 0.7739 (m-80)
  outliers start: 35
  outliers final: 29
  residues processed: 94
  average time/residue: 0.0740
  time to fit residues: 9.9337
Evaluate side-chains
  92 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 63
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  250 GLN
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  410 GLU
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  493 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 49 optimal weight:    8.9990
   chunk 60 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 66 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 40 optimal weight:    0.2980
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.9984

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.144519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.116904 restraints weight = 8445.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.10
r_work: 0.3226 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7850  Z= 0.116
  Angle     :  0.493   9.991  10670  Z= 0.246
  Chirality :  0.044   0.144   1190
  Planarity :  0.004   0.048   1338
  Dihedral  : 11.208 109.640   1310
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 16.33 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.27), residues: 964
  helix:  1.94 (0.31), residues: 280
  sheet: -0.04 (0.36), residues: 230
  loop : -1.52 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 139 
 TYR   0.022   0.001   TYR A 200 
 PHE   0.014   0.001   PHE A 208 
 TRP   0.006   0.001   TRP B  88 
 HIS   0.001   0.001   HIS B  96 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.12 ( 7850)
  covalent geometry    : angle       0.49259 /  0.25 (10670)
  hydrogen bonds       : bond        0.04066 /  2.63 (  273)
  hydrogen bonds       : angle       4.05905 /  2.80 (  768)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 57
  time to evaluate  : 0.273 
Fit side-chains
REVERT: B   29 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7790 (mttp)
REVERT: B  116 TYR cc_start: 0.7539 (m-80) cc_final: 0.7067 (m-80)
REVERT: B  128 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6857 (tm-30)
REVERT: B  394 PHE cc_start: 0.7894 (m-80) cc_final: 0.7662 (m-80)
REVERT: A   29 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7770 (mttp)
REVERT: A  116 TYR cc_start: 0.7633 (m-80) cc_final: 0.7202 (m-80)
REVERT: A  128 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6863 (tm-30)
REVERT: A  394 PHE cc_start: 0.7901 (m-80) cc_final: 0.7675 (m-80)
  outliers start: 42
  outliers final: 34
  residues processed: 92
  average time/residue: 0.0713
  time to fit residues: 9.3675
Evaluate side-chains
  95 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 57
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 LYS
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  410 GLU
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  250 GLN
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  410 GLU
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  493 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 12 optimal weight:    0.1980
   chunk 1 optimal weight:    8.9990
   chunk 72 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.9382

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.144755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.117150 restraints weight = 8378.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 2.09
r_work: 0.3239 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7850  Z= 0.110
  Angle     :  0.486   9.996  10670  Z= 0.243
  Chirality :  0.044   0.145   1190
  Planarity :  0.004   0.047   1338
  Dihedral  : 11.173 110.100   1310
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 16.96 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.27), residues: 964
  helix:  1.95 (0.30), residues: 280
  sheet: -0.01 (0.36), residues: 230
  loop : -1.46 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 139 
 TYR   0.022   0.001   TYR A 200 
 PHE   0.013   0.001   PHE A 208 
 TRP   0.006   0.001   TRP B  88 
 HIS   0.001   0.000   HIS B  96 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.11 ( 7850)
  covalent geometry    : angle       0.48584 /  0.24 (10670)
  hydrogen bonds       : bond        0.03939 /  2.55 (  273)
  hydrogen bonds       : angle       4.04750 /  2.79 (  768)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 58
  time to evaluate  : 0.286 
Fit side-chains
REVERT: B   29 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7788 (mttp)
REVERT: B  116 TYR cc_start: 0.7527 (m-80) cc_final: 0.7055 (m-80)
REVERT: B  128 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7126 (tm-30)
REVERT: B  394 PHE cc_start: 0.7878 (m-80) cc_final: 0.7641 (m-80)
REVERT: A   29 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7792 (mttp)
REVERT: A  116 TYR cc_start: 0.7640 (m-80) cc_final: 0.7224 (m-80)
REVERT: A  128 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6871 (tm-30)
REVERT: A  394 PHE cc_start: 0.7886 (m-80) cc_final: 0.7640 (m-80)
  outliers start: 38
  outliers final: 33
  residues processed: 89
  average time/residue: 0.0765
  time to fit residues: 9.7452
Evaluate side-chains
  94 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 57
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 LYS
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  410 GLU
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  250 GLN
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  410 GLU
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  493 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 44 optimal weight:    0.4980
   chunk 37 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.6986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.142231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.114336 restraints weight = 8493.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 2.11
r_work: 0.3100 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8732
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7850  Z= 0.167
  Angle     :  0.547  10.065  10670  Z= 0.275
  Chirality :  0.046   0.149   1190
  Planarity :  0.004   0.048   1338
  Dihedral  : 12.120 113.334   1310
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 17.59 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.27), residues: 964
  helix:  1.82 (0.30), residues: 282
  sheet: -0.12 (0.36), residues: 230
  loop : -1.55 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 293 
 TYR   0.023   0.002   TYR B 200 
 PHE   0.020   0.002   PHE A 208 
 TRP   0.008   0.001   TRP B  88 
 HIS   0.002   0.001   HIS B  96 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00417 /  0.17 ( 7850)
  covalent geometry    : angle       0.54692 /  0.27 (10670)
  hydrogen bonds       : bond        0.05086 /  3.28 (  273)
  hydrogen bonds       : angle       4.24915 /  2.94 (  768)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 54
  time to evaluate  : 0.268 
Fit side-chains
REVERT: B   29 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7834 (mttp)
REVERT: B  116 TYR cc_start: 0.7659 (m-80) cc_final: 0.7306 (m-80)
REVERT: B  128 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7144 (tm-30)
REVERT: B  394 PHE cc_start: 0.7928 (m-80) cc_final: 0.7670 (m-80)
REVERT: A   29 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7830 (mttp)
REVERT: A  116 TYR cc_start: 0.7651 (m-80) cc_final: 0.7235 (m-80)
REVERT: A  128 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7153 (tm-30)
REVERT: A  394 PHE cc_start: 0.7924 (m-80) cc_final: 0.7669 (m-80)
  outliers start: 37
  outliers final: 33
  residues processed: 88
  average time/residue: 0.0691
  time to fit residues: 8.7741
Evaluate side-chains
  86 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 49
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 LYS
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  410 GLU
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  250 GLN
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  410 GLU
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  493 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 91 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 85 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.0582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.144025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.116229 restraints weight = 8371.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 2.10
r_work: 0.3225 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.1889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7850  Z= 0.119
  Angle     :  0.498  10.209  10670  Z= 0.250
  Chirality :  0.045   0.151   1190
  Planarity :  0.004   0.046   1338
  Dihedral  : 11.722 111.690   1310
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 17.96 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.27), residues: 964
  helix:  1.90 (0.30), residues: 282
  sheet: -0.01 (0.36), residues: 230
  loop : -1.51 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 139 
 TYR   0.022   0.001   TYR A 200 
 PHE   0.014   0.001   PHE B 208 
 TRP   0.006   0.001   TRP B  88 
 HIS   0.001   0.000   HIS B  96 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 ( 7850)
  covalent geometry    : angle       0.49805 /  0.25 (10670)
  hydrogen bonds       : bond        0.04175 /  2.70 (  273)
  hydrogen bonds       : angle       4.13382 /  2.85 (  768)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 56
  time to evaluate  : 0.277 
Fit side-chains
REVERT: B   29 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7799 (mttp)
REVERT: B  116 TYR cc_start: 0.7562 (m-80) cc_final: 0.7103 (m-80)
REVERT: B  394 PHE cc_start: 0.7895 (m-80) cc_final: 0.7649 (m-80)
REVERT: A   29 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7793 (mttp)
REVERT: A  116 TYR cc_start: 0.7595 (m-80) cc_final: 0.7167 (m-80)
REVERT: A  394 PHE cc_start: 0.7931 (m-80) cc_final: 0.7690 (m-80)
  outliers start: 36
  outliers final: 33
  residues processed: 87
  average time/residue: 0.0778
  time to fit residues: 9.5083
Evaluate side-chains
  88 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 53
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 LYS
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  410 GLU
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  250 GLN
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  410 GLU
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  493 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0470
   chunk 0 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0470
   chunk 10 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 87 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0980
   overall best weight:    0.3576

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  81 GLN
A  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.148620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.121161 restraints weight = 8332.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.08
r_work: 0.3295 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3148 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7850  Z= 0.077
  Angle     :  0.443  10.076  10670  Z= 0.221
  Chirality :  0.043   0.145   1190
  Planarity :  0.004   0.048   1338
  Dihedral  : 10.392 106.815   1310
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 19.10 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.28), residues: 964
  helix:  2.10 (0.31), residues: 280
  sheet:  0.37 (0.38), residues: 220
  loop : -1.35 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 139 
 TYR   0.021   0.001   TYR A 200 
 PHE   0.008   0.001   PHE A 406 
 TRP   0.009   0.001   TRP B  98 
 HIS   0.001   0.000   HIS A 108 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00165 /  0.08 ( 7850)
  covalent geometry    : angle       0.44279 /  0.22 (10670)
  hydrogen bonds       : bond        0.02819 /  1.84 (  273)
  hydrogen bonds       : angle       3.91300 /  2.69 (  768)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1731.39 seconds
wall clock time: 30 minutes 24.07 seconds (1824.07 seconds total)