Starting phenix.real_space_refine
on Sat May  2 14:09:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vcl_64957/05_2026/9vcl_64957.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vcl_64957/05_2026/9vcl_64957.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vcl_64957/05_2026/9vcl_64957.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vcl_64957/05_2026/9vcl_64957.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vcl_64957/05_2026/9vcl_64957.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vcl_64957/05_2026/9vcl_64957.cif"
  }
  resolution = 3.08
  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=   0.028
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: 8
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      5      6.06       5
     P      55      5.49       5
     S      52      5.16       5
     C    3743      2.51       5
     N    1056      2.21       5
     O    1306      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6220
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 955
          Classifications: {'peptide': 131}
          Link IDs: {'PTRANS': 7, 'TRANS': 123}
    Chain: "B"
      Number of atoms: 4089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 4089
          Classifications: {'peptide': 512}
          Link IDs: {'PTRANS': 26, 'TRANS': 485}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 546
          Classifications: {'RNA': 26}
          Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 14}
          Link IDs: {'rna3p': 25}
    Chain: "T"
      Number of atoms: 596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 596
          Classifications: {'RNA': 28}
          Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 13}
          Link IDs: {'rna3p': 27}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {' CA': 2, ' ZN': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "P"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'EIF': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    520  SG  CYS A  74      37.113  23.394  44.080  1.00 41.73           S
  ATOM    546  SG  CYS A  77      40.727  24.949  43.307  1.00 43.10           S
  ATOM    651  SG  CYS A  90      39.528  22.020  41.919  1.00 53.02           S
  ATOM   2581  SG  CYS B 207      33.917  21.184  76.044  1.00 40.24           S
  ATOM   2601  SG  CYS B 210      31.737  21.485  79.938  1.00 50.80           S
  ATOM   2722  SG  CYS B 226      35.695  23.025  78.375  1.00 33.31           S
  ATOM   3022  SG  CYS B 261      53.283  51.455  82.167  1.00 60.41           S
  ATOM   3152  SG  CYS B 279      50.229  49.907  79.979  1.00 33.40           S
  ATOM   4542  SG  CYS B 452      30.429  34.066 127.830  1.00124.04           S
  ATOM   4698  SG  CYS B 484      31.964  32.968 125.423  1.00132.93           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   EIF P 101 " occ=0.97
      ... (22 atoms not shown)
      pdb=" P   EIF P 101 " occ=0.97
  Time building chain proxies: 1.41, per 1000 atoms: 0.23
  Number of scatterers: 6220
  At special positions: 0
  Unit cell: (77.38, 99.28, 139.43, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Zn      5     29.99
     Ca      2     19.99
     S      52     16.00
     P      55     15.00
     F       1      9.00
     O    1306      8.00
     N    1056      7.00
     C    3743      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 206.3 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 201 "
        pdb="ZN    ZN A 201 " - pdb=" NE2 HIS A  83 "
        pdb="ZN    ZN A 201 " - pdb=" SG  CYS A  90 "
        pdb="ZN    ZN A 201 " - pdb=" SG  CYS A  77 "
        pdb="ZN    ZN A 201 " - pdb=" SG  CYS A  74 "
      pdb="  ZN B 603 "
        pdb="ZN    ZN B 603 " - pdb=" ND1 HIS B 229 "
        pdb="ZN    ZN B 603 " - pdb=" SG  CYS B 207 "
        pdb="ZN    ZN B 603 " - pdb=" SG  CYS B 226 "
        pdb="ZN    ZN B 603 " - pdb=" SG  CYS B 210 "
      pdb="  ZN B 604 "
        pdb="ZN    ZN B 604 " - pdb=" ND1 HIS B 264 "
        pdb="ZN    ZN B 604 " - pdb=" NE2 HIS B 257 "
        pdb="ZN    ZN B 604 " - pdb=" SG  CYS B 279 "
        pdb="ZN    ZN B 604 " - pdb=" SG  CYS B 261 "
      pdb="  ZN B 605 "
        pdb="ZN    ZN B 605 " - pdb=" SG  CYS B 452 "
        pdb="ZN    ZN B 605 " - pdb=" ND1 HIS B 487 "
        pdb="ZN    ZN B 605 " - pdb=" SG  CYS B 484 "
      Number of angles added : 8


  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1202

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 9 sheets defined
      26.9% alpha, 13.8% beta
      23 base pairs and 37 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 18
    Processing helix  chain 'A' and resid 24 through 33
      removed outlier: 3.537A  pdb=" N   ASP A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   TYR A  30 " --> pdb=" O   ALA A  26 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU A  31 " --> pdb=" O   TYR A  27 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ALA A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 74
    Processing helix  chain 'A' and resid 75 through 80
    Processing helix  chain 'A' and resid 85 through 89
      removed outlier: 4.119A  pdb=" N   PHE A  89 " --> pdb=" O   PRO A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 104
      No H-bonds generated for 'chain 'A' and resid 102 through 104'
    Processing helix  chain 'A' and resid 106 through 114
      removed outlier: 4.028A  pdb=" N   LEU A 112 " --> pdb=" O   VAL A 108 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LYS A 113 " --> pdb=" O   GLY A 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 80
    Processing helix  chain 'B' and resid 149 through 153
      removed outlier: 3.793A  pdb=" N   MET B 153 " --> pdb=" O   ILE B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 163
    Processing helix  chain 'B' and resid 163 through 174
      removed outlier: 3.693A  pdb=" N   VAL B 167 " --> pdb=" O   ARG B 163 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   ASP B 172 " --> pdb=" O   GLN B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 194
      removed outlier: 3.678A  pdb=" N   THR B 193 " --> pdb=" O   GLY B 189 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER B 194 " --> pdb=" O   PHE B 190 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 189 through 194'
    Processing helix  chain 'B' and resid 245 through 248
      removed outlier: 3.699A  pdb=" N   GLY B 248 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 245 through 248'
    Processing helix  chain 'B' and resid 253 through 258
      removed outlier: 3.677A  pdb=" N   ASP B 258 " --> pdb=" O   GLN B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 287
      removed outlier: 3.666A  pdb=" N   ALA B 281 " --> pdb=" O   THR B 277 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   HIS B 283 " --> pdb=" O   CYS B 279 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLU B 284 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 325
      removed outlier: 3.507A  pdb=" N   VAL B 317 " --> pdb=" O   GLN B 313 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LYS B 318 " --> pdb=" O   HIS B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 374
    Processing helix  chain 'B' and resid 432 through 437
      removed outlier: 3.807A  pdb=" N   VAL B 437 " --> pdb=" O   SER B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 480
    Processing helix  chain 'B' and resid 487 through 505
    Processing helix  chain 'B' and resid 516 through 523
      removed outlier: 3.952A  pdb=" N   ASN B 521 " --> pdb=" O   ASN B 518 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56
    Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 35
      removed outlier: 3.534A  pdb=" N   THR B  35 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU B  38 " --> pdb=" O   THR B  35 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 115 through 118
      removed outlier: 3.741A  pdb=" N   VAL B 115 " --> pdb=" O   PHE B 111 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE B 111 " --> pdb=" O   VAL B 115 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   ASN B 104 " --> pdb=" O   ALA B  96 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ALA B  96 " --> pdb=" O   ASN B 104 " (cutoff:3.500A)
      removed outlier: 5.772A  pdb=" N   CYS B  94 " --> pdb=" O   PRO B 106 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 115 through 118
      removed outlier: 3.741A  pdb=" N   VAL B 115 " --> pdb=" O   PHE B 111 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE B 111 " --> pdb=" O   VAL B 115 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   ASN B 104 " --> pdb=" O   ALA B  96 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ALA B  96 " --> pdb=" O   ASN B 104 " (cutoff:3.500A)
      removed outlier: 5.772A  pdb=" N   CYS B  94 " --> pdb=" O   PRO B 106 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   PHE B  89 " --> pdb=" O   VAL B 184 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   PHE B 183 " --> pdb=" O   ILE B 242 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 122 through 123
      removed outlier: 3.664A  pdb=" N   SER B 134 " --> pdb=" O   GLY B 123 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 364 through 365
      removed outlier: 7.711A  pdb=" N   GLU B 364 " --> pdb=" O   TRP B 348 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   PHE B 350 " --> pdb=" O   GLU B 364 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   LEU B 329 " --> pdb=" O   LYS B 349 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   TYR B 351 " --> pdb=" O   LEU B 329 " (cutoff:3.500A)
      removed outlier: 5.974A  pdb=" N   ASP B 331 " --> pdb=" O   TYR B 351 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL B 381 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 397 through 401
    Processing sheet with id=AA8, first strand: chain 'B' and resid 410 through 412
    Processing sheet with id=AA9, first strand: chain 'B' and resid 446 through 447
      removed outlier: 6.328A  pdb=" N   TYR B 446 " --> pdb=" O   ILE B 474 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    111 hydrogen bonds defined for protein.
    300 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      48 hydrogen bonds
      80 hydrogen bond angles
      0 basepair planarities
      23 basepair parallelities
      37 stacking parallelities
  Total time for adding SS restraints: 0.92

  Time building geometry restraints manager: 0.48 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 875
        1.30 -     1.43: 2143
        1.43 -     1.56: 3287
        1.56 -     1.68: 111
        1.68 -     1.81: 68
  Bond restraints: 6484
  Sorted by residual:
  bond pdb=" C2  EIF P 101 "
       pdb=" C3  EIF P 101 "
    ideal  model  delta    sigma   weight residual
    1.542  1.312  0.230 2.00e-02 2.50e+03 1.32e+02
  bond pdb=" C3  EIF P 101 "
       pdb=" O5  EIF P 101 "
    ideal  model  delta    sigma   weight residual
    1.462  1.652 -0.190 2.00e-02 2.50e+03 9.01e+01
  bond pdb=" CA  ASP B 273 "
       pdb=" C   ASP B 273 "
    ideal  model  delta    sigma   weight residual
    1.524  1.421  0.103 1.24e-02 6.50e+03 6.90e+01
  bond pdb=" CA  ALA B 274 "
       pdb=" CB  ALA B 274 "
    ideal  model  delta    sigma   weight residual
    1.537  1.425  0.112 1.38e-02 5.25e+03 6.61e+01
  bond pdb=" CA  ALA A  71 "
       pdb=" C   ALA A  71 "
    ideal  model  delta    sigma   weight residual
    1.524  1.423  0.101 1.29e-02 6.01e+03 6.12e+01
  ... (remaining 6479 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.36: 9035
        7.36 -    14.73: 22
       14.73 -    22.09: 7
       22.09 -    29.46: 1
       29.46 -    36.82: 1
  Bond angle restraints: 9066
  Sorted by residual:
  angle pdb=" N   GLY B 265 "
        pdb=" CA  GLY B 265 "
        pdb=" C   GLY B 265 "
      ideal   model   delta    sigma   weight residual
     113.18  150.00  -36.82 2.37e+00 1.78e-01 2.41e+02
  angle pdb=" N   ASN B 266 "
        pdb=" CA  ASN B 266 "
        pdb=" C   ASN B 266 "
      ideal   model   delta    sigma   weight residual
     107.75   83.67   24.08 1.86e+00 2.89e-01 1.68e+02
  angle pdb=" C   ARG B  76 "
        pdb=" CA  ARG B  76 "
        pdb=" CB  ARG B  76 "
      ideal   model   delta    sigma   weight residual
     110.68  131.17  -20.49 1.70e+00 3.46e-01 1.45e+02
  angle pdb=" N   ASP B 273 "
        pdb=" CA  ASP B 273 "
        pdb=" C   ASP B 273 "
      ideal   model   delta    sigma   weight residual
     113.19   95.38   17.81 1.58e+00 4.01e-01 1.27e+02
  angle pdb=" N   ASN B 238 "
        pdb=" CA  ASN B 238 "
        pdb=" C   ASN B 238 "
      ideal   model   delta    sigma   weight residual
     108.12   87.62   20.50 1.97e+00 2.58e-01 1.08e+02
  ... (remaining 9061 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 3324
       17.92 -    35.83: 364
       35.83 -    53.75: 111
       53.75 -    71.67: 61
       71.67 -    89.58: 9
  Dihedral angle restraints: 3869
    sinusoidal: 1997
      harmonic: 1872
  Sorted by residual:
  dihedral pdb=" C   VAL B 287 "
           pdb=" N   VAL B 287 "
           pdb=" CA  VAL B 287 "
           pdb=" CB  VAL B 287 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -149.34   27.34     0      2.50e+00 1.60e-01 1.20e+02
  dihedral pdb=" C   ARG B  76 "
           pdb=" N   ARG B  76 "
           pdb=" CA  ARG B  76 "
           pdb=" CB  ARG B  76 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -148.76   26.16     0      2.50e+00 1.60e-01 1.09e+02
  dihedral pdb=" N   ASN B 266 "
           pdb=" C   ASN B 266 "
           pdb=" CA  ASN B 266 "
           pdb=" CB  ASN B 266 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80   97.03   25.77     0      2.50e+00 1.60e-01 1.06e+02
  ... (remaining 3866 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.226: 1033
       0.226 -    0.452: 3
       0.452 -    0.678: 3
       0.678 -    0.904: 1
       0.904 -    1.130: 3
  Chirality restraints: 1043
  Sorted by residual:
  chirality pdb=" CA  TYR B 237 "
            pdb=" N   TYR B 237 "
            pdb=" C   TYR B 237 "
            pdb=" CB  TYR B 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.38    1.13 2.00e-01 2.50e+01 3.19e+01
  chirality pdb=" CA  ARG B  76 "
            pdb=" N   ARG B  76 "
            pdb=" C   ARG B  76 "
            pdb=" CB  ARG B  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.50    1.01 2.00e-01 2.50e+01 2.56e+01
  chirality pdb=" CA  VAL B 287 "
            pdb=" N   VAL B 287 "
            pdb=" C   VAL B 287 "
            pdb=" CB  VAL B 287 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.45    0.99 2.00e-01 2.50e+01 2.43e+01
  ... (remaining 1040 not shown)

  Planarity restraints: 959
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  68 "    0.016 2.00e-02 2.50e+03   3.11e-02 9.66e+00
        pdb=" C   PHE A  68 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   PHE A  68 "    0.020 2.00e-02 2.50e+03
        pdb=" N   GLY A  69 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B  19 "    0.036 5.00e-02 4.00e+02   5.49e-02 4.83e+00
        pdb=" N   PRO B  20 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B  20 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B  20 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 120 "    0.034 5.00e-02 4.00e+02   5.15e-02 4.24e+00
        pdb=" N   PRO B 121 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO B 121 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 121 "    0.029 5.00e-02 4.00e+02
  ... (remaining 956 not shown)

  Histogram of nonbonded interaction distances:
        1.83 -     2.44: 40
        2.44 -     3.06: 4150
        3.06 -     3.67: 9941
        3.67 -     4.29: 14666
        4.29 -     4.90: 22880
  Nonbonded interactions: 51677
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B  90 "
            pdb="CA    CA B 601 "
     model   vdw
     1.826 2.510
  nonbonded pdb=" OE2 GLU B  92 "
            pdb="CA    CA B 601 "
     model   vdw
     1.844 2.510
  nonbonded pdb=" OD2 ASP B 273 "
            pdb="CA    CA B 601 "
     model   vdw
     1.921 2.510
  nonbonded pdb=" O   LYS B 200 "
            pdb=" O   TYR B 237 "
     model   vdw
     1.948 3.040
  nonbonded pdb=" OG1 THR B 127 "
            pdb=" O   ASN B 130 "
     model   vdw
     2.148 3.040
  ... (remaining 51672 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.97 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:             4.010
  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:                     7.650
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
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      :  0.014   0.529   6500  Z= 0.716
  Angle     :  1.308  36.822   9074  Z= 0.703
  Chirality :  0.084   1.130   1043
  Planarity :  0.005   0.055    959
  Dihedral  : 17.658  89.582   2667
  Min Nonbonded Distance : 1.826

Molprobity Statistics.
  All-atom Clashscore : 19.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 13.00 %
    Favored  : 85.02 %
  Cbeta Deviations :  1.83 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.52 (0.27), residues: 637
  helix: -3.23 (0.33), residues: 141
  sheet: -3.89 (0.56), residues: 57
  loop : -2.99 (0.25), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 213 
 TYR   0.020   0.002   TYR B  69 
 PHE   0.035   0.003   PHE B 190 
 TRP   0.015   0.002   TRP B 159 
 HIS   0.005   0.001   HIS B 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.01201 ( 6484)
  covalent geometry    : angle       1.24091 ( 9066)
  hydrogen bonds       : bond        0.29700 (  153)
  hydrogen bonds       : angle       9.48386 (  380)
  metal coordination   : bond        0.15815 (   15)
  metal coordination   : angle      13.99856 (    8)
  Misc. bond           : bond        0.15399 (    1)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7625 (mt0)
REVERT: A  103 CYS cc_start: 0.8161 (m) cc_final: 0.7937 (m)
REVERT: B  352 ASP cc_start: 0.6838 (m-30) cc_final: 0.6369 (p0)
  outliers start: 11
  outliers final: 2
  residues processed: 128
  average time/residue: 0.0992
  time to fit residues: 15.7676
Evaluate side-chains
  74 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  268 HIS
Chi-restraints excluded: chain B residue  288 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.4980
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
A  40 ASN
A  53 GLN
A  98 GLN
A 114 ASN
B  22 GLN
B  67 ASN
B  95 HIS
B 108 GLN
B 116 ASN
B 188 HIS
** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 256 ASN
B 486 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.143542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.089734 restraints weight = 10403.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 2.32
r_work: 0.3047 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2896
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.99   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.2608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.084   6500  Z= 0.266
  Angle     :  0.735  11.197   9074  Z= 0.368
  Chirality :  0.044   0.255   1043
  Planarity :  0.005   0.051    959
  Dihedral  : 16.515  73.589   1525
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 15.88 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.59 (0.28), residues: 637
  helix: -2.40 (0.36), residues: 146
  sheet: -2.65 (0.66), residues: 55
  loop : -2.49 (0.26), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  98 
 TYR   0.014   0.002   TYR B 224 
 PHE   0.020   0.002   PHE A  19 
 TRP   0.016   0.002   TRP B 159 
 HIS   0.005   0.001   HIS B 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00613 ( 6484)
  covalent geometry    : angle       0.71995 ( 9066)
  hydrogen bonds       : bond        0.09060 (  153)
  hydrogen bonds       : angle       5.49695 (  380)
  metal coordination   : bond        0.02939 (   15)
  metal coordination   : angle       4.96459 (    8)
  Misc. bond           : bond        0.00049 (    1)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A   56 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8496 (m)
REVERT: A   89 PHE cc_start: 0.8657 (m-10) cc_final: 0.8410 (m-80)
REVERT: A  106 ASP cc_start: 0.8262 (p0) cc_final: 0.7784 (p0)
REVERT: B   38 LEU cc_start: 0.8432 (mp) cc_final: 0.8186 (mt)
REVERT: B  268 HIS cc_start: 0.6885 (OUTLIER) cc_final: 0.6614 (m170)
REVERT: B  302 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7437 (mp0)
REVERT: B  352 ASP cc_start: 0.7216 (m-30) cc_final: 0.6083 (p0)
  outliers start: 22
  outliers final: 11
  residues processed: 93
  average time/residue: 0.0738
  time to fit residues: 9.2383
Evaluate side-chains
  81 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ASN
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   72 SER
Chi-restraints excluded: chain A residue  113 LYS
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  268 HIS
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  382 CYS
Chi-restraints excluded: chain B residue  387 CYS
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 57 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 20 optimal weight:    0.2980
   chunk 27 optimal weight:    0.0170
   chunk 51 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 55 optimal weight:    7.9990
   overall best weight:    0.8020

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

Flipped N/Q/H residues before XYZ refinement:
A  40 ASN
A  65 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.143637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.091995 restraints weight = 10217.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 2.60
r_work: 0.3016 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3015
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.99   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.99   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3015
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.3260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   6500  Z= 0.163
  Angle     :  0.604  10.658   9074  Z= 0.303
  Chirality :  0.040   0.154   1043
  Planarity :  0.004   0.044    959
  Dihedral  : 15.978  73.694   1521
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 18.41 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.95 (0.30), residues: 637
  helix: -1.79 (0.39), residues: 145
  sheet: -2.26 (0.69), residues: 55
  loop : -2.09 (0.27), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 212 
 TYR   0.016   0.001   TYR B 370 
 PHE   0.012   0.001   PHE A  19 
 TRP   0.011   0.001   TRP B 159 
 HIS   0.003   0.001   HIS B  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 6484)
  covalent geometry    : angle       0.59774 ( 9066)
  hydrogen bonds       : bond        0.07961 (  153)
  hydrogen bonds       : angle       4.89365 (  380)
  metal coordination   : bond        0.01528 (   15)
  metal coordination   : angle       2.98741 (    8)
  Misc. bond           : bond        0.00022 (    1)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  106 ASP cc_start: 0.7893 (p0) cc_final: 0.7573 (p0)
REVERT: B   38 LEU cc_start: 0.8617 (mp) cc_final: 0.8383 (mt)
REVERT: B  302 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7417 (mp0)
REVERT: B  370 TYR cc_start: 0.7850 (t80) cc_final: 0.7471 (t80)
REVERT: B  391 ARG cc_start: 0.8746 (mtp180) cc_final: 0.8422 (mtp180)
  outliers start: 21
  outliers final: 12
  residues processed: 89
  average time/residue: 0.0742
  time to fit residues: 9.0261
Evaluate side-chains
  77 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  382 CYS
Chi-restraints excluded: chain B residue  387 CYS
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0040
   chunk 60 optimal weight:    9.9990
   chunk 9 optimal weight:    0.6980
   chunk 48 optimal weight:    9.9990
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
A  40 ASN
B  22 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.144401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.093502 restraints weight = 10257.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.47
r_work: 0.3075 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3071
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.99   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.99   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3071
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.3746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6500  Z= 0.124
  Angle     :  0.541   9.674   9074  Z= 0.271
  Chirality :  0.038   0.150   1043
  Planarity :  0.004   0.042    959
  Dihedral  : 15.455  73.675   1519
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 19.31 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.42 (0.31), residues: 637
  helix: -1.19 (0.43), residues: 139
  sheet: -2.44 (0.73), residues: 50
  loop : -1.74 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 289 
 TYR   0.014   0.001   TYR B 368 
 PHE   0.013   0.001   PHE B 444 
 TRP   0.008   0.001   TRP B 186 
 HIS   0.004   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6484)
  covalent geometry    : angle       0.53926 ( 9066)
  hydrogen bonds       : bond        0.07656 (  153)
  hydrogen bonds       : angle       4.51316 (  380)
  metal coordination   : bond        0.00948 (   15)
  metal coordination   : angle       1.73576 (    8)
  Misc. bond           : bond        0.00024 (    1)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A   28 LYS cc_start: 0.8716 (tmtt) cc_final: 0.8233 (mtmm)
REVERT: B  352 ASP cc_start: 0.7203 (m-30) cc_final: 0.6052 (p0)
REVERT: B  370 TYR cc_start: 0.7811 (t80) cc_final: 0.7472 (t80)
REVERT: B  391 ARG cc_start: 0.8708 (mtp180) cc_final: 0.8413 (mtp180)
  outliers start: 16
  outliers final: 12
  residues processed: 90
  average time/residue: 0.0760
  time to fit residues: 9.2256
Evaluate side-chains
  82 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  113 LYS
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  382 CYS
Chi-restraints excluded: chain B residue  387 CYS
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    0.4980
   chunk 46 optimal weight:    0.0570
   chunk 42 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 65 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A  40 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.143991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.088689 restraints weight = 10290.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 2.31
r_work: 0.3073 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2921
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.99   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2921
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.4006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6500  Z= 0.122
  Angle     :  0.533  10.328   9074  Z= 0.263
  Chirality :  0.039   0.149   1043
  Planarity :  0.004   0.042    959
  Dihedral  : 15.325  73.720   1519
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 20.40 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.18 (0.31), residues: 637
  helix: -0.94 (0.44), residues: 139
  sheet: -2.32 (0.66), residues: 56
  loop : -1.57 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  98 
 TYR   0.014   0.001   TYR B 498 
 PHE   0.012   0.001   PHE B 444 
 TRP   0.007   0.001   TRP B 159 
 HIS   0.003   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6484)
  covalent geometry    : angle       0.53035 ( 9066)
  hydrogen bonds       : bond        0.07527 (  153)
  hydrogen bonds       : angle       4.41203 (  380)
  metal coordination   : bond        0.00885 (   15)
  metal coordination   : angle       1.78108 (    8)
  Misc. bond           : bond        0.00026 (    1)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A   28 LYS cc_start: 0.8805 (tmtt) cc_final: 0.8345 (mtmm)
REVERT: A  113 LYS cc_start: 0.8690 (ttmt) cc_final: 0.8394 (mtpt)
REVERT: B  352 ASP cc_start: 0.7366 (m-30) cc_final: 0.6188 (p0)
REVERT: B  370 TYR cc_start: 0.7919 (t80) cc_final: 0.7606 (t80)
REVERT: B  391 ARG cc_start: 0.8777 (mtp180) cc_final: 0.8515 (mtp180)
  outliers start: 17
  outliers final: 14
  residues processed: 83
  average time/residue: 0.0721
  time to fit residues: 8.2396
Evaluate side-chains
  83 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 42 optimal weight:    0.0570
   chunk 52 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A  40 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.144412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.091903 restraints weight = 10141.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 2.49
r_work: 0.3038 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3042
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3042 r_free = 0.3042    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3042 r_free = 0.3042    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3042
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.4186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6500  Z= 0.121
  Angle     :  0.521  10.488   9074  Z= 0.256
  Chirality :  0.038   0.150   1043
  Planarity :  0.003   0.042    959
  Dihedral  : 15.190  73.736   1519
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 19.31 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.97 (0.32), residues: 637
  helix: -0.84 (0.44), residues: 142
  sheet: -2.14 (0.64), residues: 58
  loop : -1.41 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  98 
 TYR   0.017   0.001   TYR B 368 
 PHE   0.015   0.001   PHE B 444 
 TRP   0.008   0.001   TRP B 186 
 HIS   0.003   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6484)
  covalent geometry    : angle       0.51879 ( 9066)
  hydrogen bonds       : bond        0.07390 (  153)
  hydrogen bonds       : angle       4.41857 (  380)
  metal coordination   : bond        0.00963 (   15)
  metal coordination   : angle       1.71958 (    8)
  Misc. bond           : bond        0.00024 (    1)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A   28 LYS cc_start: 0.8726 (tmtt) cc_final: 0.8351 (mtmm)
REVERT: B   49 MET cc_start: 0.8376 (mpp) cc_final: 0.8155 (tmm)
REVERT: B  352 ASP cc_start: 0.7237 (m-30) cc_final: 0.6081 (p0)
REVERT: B  370 TYR cc_start: 0.7880 (t80) cc_final: 0.7433 (t80)
REVERT: B  391 ARG cc_start: 0.8700 (mtp180) cc_final: 0.8416 (mtp180)
  outliers start: 20
  outliers final: 16
  residues processed: 85
  average time/residue: 0.0646
  time to fit residues: 7.5713
Evaluate side-chains
  83 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  387 CYS
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0980
   chunk 29 optimal weight:    0.9990
   chunk 10 optimal weight:    0.1980
   chunk 2 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 67 optimal weight:   10.0000
   chunk 49 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  40 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.144426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.090631 restraints weight = 10116.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 2.25
r_work: 0.3075 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2922
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2922 r_free = 0.2922    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2922 r_free = 0.2922    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2922
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.4330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6500  Z= 0.116
  Angle     :  0.514  10.084   9074  Z= 0.256
  Chirality :  0.038   0.148   1043
  Planarity :  0.004   0.044    959
  Dihedral  : 15.099  73.712   1519
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 19.13 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.83 (0.32), residues: 637
  helix: -0.73 (0.44), residues: 142
  sheet: -2.05 (0.65), residues: 58
  loop : -1.31 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  98 
 TYR   0.016   0.001   TYR B 368 
 PHE   0.011   0.001   PHE B 444 
 TRP   0.008   0.001   TRP B 186 
 HIS   0.002   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6484)
  covalent geometry    : angle       0.51217 ( 9066)
  hydrogen bonds       : bond        0.07341 (  153)
  hydrogen bonds       : angle       4.35498 (  380)
  metal coordination   : bond        0.00855 (   15)
  metal coordination   : angle       1.63523 (    8)
  Misc. bond           : bond        0.00024 (    1)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.8807 (tmtt) cc_final: 0.8362 (mtmm)
REVERT: B   49 MET cc_start: 0.8600 (mpp) cc_final: 0.8229 (tmm)
REVERT: B  352 ASP cc_start: 0.7354 (m-30) cc_final: 0.6143 (p0)
  outliers start: 24
  outliers final: 18
  residues processed: 87
  average time/residue: 0.0724
  time to fit residues: 8.6008
Evaluate side-chains
  84 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  285 CYS
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  387 CYS
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 64 optimal weight:   20.0000
   chunk 56 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  40 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.143483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.090127 restraints weight = 10145.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.57
r_work: 0.3003 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3005
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3005
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.4459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6500  Z= 0.139
  Angle     :  0.519  10.844   9074  Z= 0.256
  Chirality :  0.039   0.151   1043
  Planarity :  0.004   0.044    959
  Dihedral  : 15.042  73.805   1519
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 18.77 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.69 (0.32), residues: 637
  helix: -0.63 (0.44), residues: 142
  sheet: -1.89 (0.65), residues: 58
  loop : -1.21 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  98 
 TYR   0.015   0.001   TYR B 368 
 PHE   0.013   0.001   PHE A  19 
 TRP   0.011   0.001   TRP B 186 
 HIS   0.004   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6484)
  covalent geometry    : angle       0.51615 ( 9066)
  hydrogen bonds       : bond        0.07212 (  153)
  hydrogen bonds       : angle       4.42795 (  380)
  metal coordination   : bond        0.01057 (   15)
  metal coordination   : angle       2.01427 (    8)
  Misc. bond           : bond        0.00019 (    1)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.8727 (tmtt) cc_final: 0.8259 (mtmm)
REVERT: B   49 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8160 (tmm)
REVERT: B  352 ASP cc_start: 0.7253 (m-30) cc_final: 0.6094 (p0)
  outliers start: 23
  outliers final: 18
  residues processed: 85
  average time/residue: 0.0719
  time to fit residues: 8.2074
Evaluate side-chains
  85 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain B residue   49 MET
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  285 CYS
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  387 CYS
Chi-restraints excluded: chain B residue  406 LEU
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 56 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0270
   chunk 58 optimal weight:    0.0770
   chunk 52 optimal weight:    2.9990
   chunk 50 optimal weight:    8.9990
   chunk 47 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 54 optimal weight:    0.4980
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
A  40 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.144928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.092950 restraints weight = 10189.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 2.66
r_work: 0.3007 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3010
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3010
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.4617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6500  Z= 0.101
  Angle     :  0.511  10.058   9074  Z= 0.249
  Chirality :  0.038   0.148   1043
  Planarity :  0.003   0.042    959
  Dihedral  : 14.975  73.608   1519
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 19.31 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.55 (0.32), residues: 637
  helix: -0.41 (0.44), residues: 142
  sheet: -1.75 (0.65), residues: 58
  loop : -1.17 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  98 
 TYR   0.016   0.001   TYR B 368 
 PHE   0.017   0.001   PHE B 444 
 TRP   0.009   0.001   TRP B 348 
 HIS   0.004   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 6484)
  covalent geometry    : angle       0.50836 ( 9066)
  hydrogen bonds       : bond        0.07234 (  153)
  hydrogen bonds       : angle       4.28960 (  380)
  metal coordination   : bond        0.00577 (   15)
  metal coordination   : angle       1.69552 (    8)
  Misc. bond           : bond        0.00021 (    1)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.8720 (tmtt) cc_final: 0.8293 (mtpp)
REVERT: B   49 MET cc_start: 0.8480 (mpp) cc_final: 0.8190 (tmm)
REVERT: B  351 TYR cc_start: 0.7992 (m-80) cc_final: 0.7735 (m-10)
REVERT: B  352 ASP cc_start: 0.7252 (m-30) cc_final: 0.6079 (p0)
  outliers start: 21
  outliers final: 18
  residues processed: 85
  average time/residue: 0.0746
  time to fit residues: 8.4326
Evaluate side-chains
  84 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  285 CYS
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  382 CYS
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  387 CYS
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 46 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0000
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.5784

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

Flipped N/Q/H residues before XYZ refinement:
A  40 ASN
B 438 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.144120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.088304 restraints weight = 10060.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.32
r_work: 0.3069 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2913 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2912
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2912 r_free = 0.2912    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2912 r_free = 0.2912    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.99   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2912
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.4739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6500  Z= 0.120
  Angle     :  0.518  10.422   9074  Z= 0.252
  Chirality :  0.038   0.151   1043
  Planarity :  0.004   0.043    959
  Dihedral  : 14.927  73.739   1519
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 18.95 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.51 (0.32), residues: 637
  helix: -0.39 (0.44), residues: 142
  sheet: -1.65 (0.65), residues: 58
  loop : -1.15 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  98 
 TYR   0.016   0.001   TYR B 368 
 PHE   0.015   0.001   PHE B 444 
 TRP   0.009   0.001   TRP B 186 
 HIS   0.002   0.001   HIS B  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6484)
  covalent geometry    : angle       0.51577 ( 9066)
  hydrogen bonds       : bond        0.07069 (  153)
  hydrogen bonds       : angle       4.30633 (  380)
  metal coordination   : bond        0.00858 (   15)
  metal coordination   : angle       1.79252 (    8)
  Misc. bond           : bond        0.00021 (    1)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.8783 (tmtt) cc_final: 0.8308 (mtmm)
REVERT: B   49 MET cc_start: 0.8659 (mpp) cc_final: 0.8255 (tmm)
REVERT: B  351 TYR cc_start: 0.8077 (m-80) cc_final: 0.7821 (m-10)
REVERT: B  352 ASP cc_start: 0.7309 (m-30) cc_final: 0.6101 (p0)
  outliers start: 21
  outliers final: 20
  residues processed: 83
  average time/residue: 0.0712
  time to fit residues: 8.0192
Evaluate side-chains
  86 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  285 CYS
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  382 CYS
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  387 CYS
Chi-restraints excluded: chain B residue  406 LEU
Chi-restraints excluded: chain B residue  500 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 64 optimal weight:   20.0000
   chunk 27 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 55 optimal weight:    0.4980
   chunk 41 optimal weight:    0.0570
   chunk 49 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
A  40 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.143866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.090456 restraints weight = 10077.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.50
r_work: 0.3041 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.99   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.99   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.4806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6500  Z= 0.125
  Angle     :  0.520  10.476   9074  Z= 0.253
  Chirality :  0.038   0.151   1043
  Planarity :  0.004   0.043    959
  Dihedral  : 14.921  73.735   1519
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 19.31 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.47 (0.33), residues: 637
  helix: -0.36 (0.44), residues: 142
  sheet: -1.60 (0.65), residues: 58
  loop : -1.13 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  98 
 TYR   0.017   0.001   TYR B 368 
 PHE   0.015   0.001   PHE B 444 
 TRP   0.008   0.001   TRP B 186 
 HIS   0.002   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6484)
  covalent geometry    : angle       0.51718 ( 9066)
  hydrogen bonds       : bond        0.06981 (  153)
  hydrogen bonds       : angle       4.31684 (  380)
  metal coordination   : bond        0.00873 (   15)
  metal coordination   : angle       1.89979 (    8)
  Misc. bond           : bond        0.00018 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2279.77 seconds
wall clock time: 39 minutes 32.25 seconds (2372.25 seconds total)