Starting phenix.real_space_refine
on Fri Oct 23 04:15:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/36cp_77389/10_2026/36cp_77389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/36cp_77389/10_2026/36cp_77389.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/36cp_77389/10_2026/36cp_77389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/36cp_77389/10_2026/36cp_77389.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/36cp_77389/10_2026/36cp_77389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/36cp_77389/10_2026/36cp_77389.map"
  }
  resolution = 1.9
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      38      5.49       5
     Mg      2      5.21       5
     S      13      5.16       5
     C    5139      2.51       5
     N    1361      2.21       5
     O    1654      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8207
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 530, 4326
          Classifications: {'peptide': 530}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 494}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "B"
      Number of atoms: 3060
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 3060
          Classifications: {'peptide': 375}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 29, 'TRANS': 345}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "F"
      Number of atoms: 743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 743
          Classifications: {'DNA': 34, 'RNA': 2}
          Modifications used: {'rna3p': 2}
          Link IDs: {'rna3p': 35}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 6
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 10
          Unusual residues: {' MG': 1, 'POP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 55
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 55
          Classifications: {'water': 55}
          Link IDs: {None: 54}
    Chain: "B"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
    Chain: "F"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb="MG    MG F 101 " occ=0.39
  Time building chain proxies: 1.77, per 1000 atoms: 0.22
  Number of scatterers: 8207
  At special positions: 0
  Unit cell: (74.23, 104.493, 122.194, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      13     16.00
     P      38     15.00
     Mg      2     11.99
     O    1654      8.00
     N    1361      7.00
     C    5139      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 380.5 milliseconds
  

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1712

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      41.1% alpha, 17.0% beta
      14 base pairs and 32 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 44
    Processing helix  chain 'A' and resid 77 through 84
    Processing helix  chain 'A' and resid 96 through 100
    Processing helix  chain 'A' and resid 114 through 118
    Processing helix  chain 'A' and resid 121 through 129
      removed outlier: 4.545A  pdb=" N   LYS A 126 " --> pdb=" O   ASP A 123 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA A 129 " --> pdb=" O   LYS A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 174
      Proline residue:  A 170  - end of helix
    Processing helix  chain 'A' and resid 194 through 212
      removed outlier: 3.739A  pdb=" N   THR A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 221
    Processing helix  chain 'A' and resid 254 through 268
    Processing helix  chain 'A' and resid 276 through 283
      removed outlier: 3.521A  pdb=" N   LEU A 282 " --> pdb=" O   GLN A 278 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 312
      removed outlier: 3.859A  pdb=" N   GLU A 312 " --> pdb=" O   GLU A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 384
    Processing helix  chain 'A' and resid 394 through 405
    Processing helix  chain 'A' and resid 473 through 489
      removed outlier: 3.502A  pdb=" N   ASP A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 508
    Processing helix  chain 'A' and resid 515 through 528
    Processing helix  chain 'B' and resid 27 through 44
    Processing helix  chain 'B' and resid 77 through 84
    Processing helix  chain 'B' and resid 112 through 118
    Processing helix  chain 'B' and resid 121 through 126
      removed outlier: 4.510A  pdb=" N   LYS B 126 " --> pdb=" O   GLU B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 129
      No H-bonds generated for 'chain 'B' and resid 127 through 129'
    Processing helix  chain 'B' and resid 134 through 138
    Processing helix  chain 'B' and resid 154 through 175
      removed outlier: 3.646A  pdb=" N   ALA B 158 " --> pdb=" O   LYS B 154 " (cutoff:3.500A)
      removed outlier: 5.109A  pdb=" N   SER B 162 " --> pdb=" O   ALA B 158 " (cutoff:3.500A)
      removed outlier: 5.383A  pdb=" N   SER B 163 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      Proline residue:  B 170  - end of helix
    Processing helix  chain 'B' and resid 194 through 210
    Processing helix  chain 'B' and resid 235 through 239
    Processing helix  chain 'B' and resid 253 through 271
      removed outlier: 3.998A  pdb=" N   GLN B 269 " --> pdb=" O   ASN B 265 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ILE B 270 " --> pdb=" O   TRP B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 283
      removed outlier: 3.922A  pdb=" N   LEU B 282 " --> pdb=" O   GLN B 278 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LEU B 283 " --> pdb=" O   LEU B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 310
    Processing helix  chain 'B' and resid 363 through 384
    Processing helix  chain 'B' and resid 394 through 406
      removed outlier: 5.662A  pdb=" N   THR B 403 " --> pdb=" O   GLU B 399 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   GLU B 404 " --> pdb=" O   THR B 400 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   TYR B 405 " --> pdb=" O   TRP B 401 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 64
    Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 109
    Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229
      removed outlier: 3.550A  pdb=" N   LYS A 238 " --> pdb=" O   HIS A 235 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 253
      removed outlier: 3.976A  pdb=" N   TRP A 252 " --> pdb=" O   ILE A 293 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 354
      removed outlier: 8.465A  pdb=" N   ASN A 348 " --> pdb=" O   GLN A 343 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   GLN A 343 " --> pdb=" O   ASN A 348 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   GLN A 336 " --> pdb=" O   GLN A 332 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   ALA A 327 " --> pdb=" O   LYS A 390 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   PHE A 389 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362
    Processing sheet with id=AA8, first strand: chain 'A' and resid 464 through 469
      removed outlier: 4.053A  pdb=" N   GLU A 438 " --> pdb=" O   GLU A 492 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 49
    Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 64
    Processing sheet with id=AB2, first strand: chain 'B' and resid 105 through 110
    Processing sheet with id=AB3, first strand: chain 'B' and resid 347 through 354
      removed outlier: 8.703A  pdb=" N   ASN B 348 " --> pdb=" O   GLN B 343 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   GLN B 343 " --> pdb=" O   ASN B 348 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   GLN B 336 " --> pdb=" O   GLN B 332 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   ALA B 327 " --> pdb=" O   LYS B 390 " (cutoff:3.500A)

    339 hydrogen bonds defined for protein.
    915 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      38 hydrogen bonds
      76 hydrogen bond angles
      0 basepair planarities
      14 basepair parallelities
      32 stacking parallelities
  Total time for adding SS restraints: 1.72

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1967
        1.33 -     1.45: 1910
        1.45 -     1.58: 4452
        1.58 -     1.70: 71
        1.70 -     1.83: 23
  Bond restraints: 8423
  Sorted by residual:
  bond pdb=" C3'  DG F  32 "
       pdb=" O3'  DG F  32 "
    ideal  model  delta    sigma   weight residual
    1.435  1.370  0.065 1.30e-02 5.92e+03 2.52e+01
  bond pdb=" C3'  DA F  -1 "
       pdb=" O3'  DA F  -1 "
    ideal  model  delta    sigma   weight residual
    1.435  1.378  0.057 1.30e-02 5.92e+03 1.94e+01
  bond pdb=" C3'  DG F  31 "
       pdb=" O3'  DG F  31 "
    ideal  model  delta    sigma   weight residual
    1.435  1.378  0.057 1.30e-02 5.92e+03 1.90e+01
  bond pdb=" C1'  DT F   8 "
       pdb=" N1   DT F   8 "
    ideal  model  delta    sigma   weight residual
    1.468  1.526 -0.058 1.40e-02 5.10e+03 1.70e+01
  bond pdb=" C3'  DC F  21 "
       pdb=" O3'  DC F  21 "
    ideal  model  delta    sigma   weight residual
    1.435  1.383  0.052 1.30e-02 5.92e+03 1.62e+01
  ... (remaining 8418 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 10373
        1.51 -     3.02: 992
        3.02 -     4.53: 200
        4.53 -     6.04: 31
        6.04 -     7.55: 5
  Bond angle restraints: 11601
  Sorted by residual:
  angle pdb=" O4'  DG F  32 "
        pdb=" C4'  DG F  32 "
        pdb=" C3'  DG F  32 "
      ideal   model   delta    sigma   weight residual
     106.00  102.49    3.51 6.00e-01 2.78e+00 3.43e+01
  angle pdb=" O2   DC F   1 "
        pdb=" C2   DC F   1 "
        pdb=" N3   DC F   1 "
      ideal   model   delta    sigma   weight residual
     121.90  117.80    4.10 7.00e-01 2.04e+00 3.43e+01
  angle pdb=" O2   DC F   3 "
        pdb=" C2   DC F   3 "
        pdb=" N3   DC F   3 "
      ideal   model   delta    sigma   weight residual
     121.90  118.28    3.62 7.00e-01 2.04e+00 2.68e+01
  angle pdb=" C4'  DC F   3 "
        pdb=" C3'  DC F   3 "
        pdb=" C2'  DC F   3 "
      ideal   model   delta    sigma   weight residual
     103.10   98.71    4.39 9.00e-01 1.23e+00 2.38e+01
  angle pdb=" C4'  DC F   1 "
        pdb=" C3'  DC F   1 "
        pdb=" C2'  DC F   1 "
      ideal   model   delta    sigma   weight residual
     103.10   98.86    4.24 9.00e-01 1.23e+00 2.22e+01
  ... (remaining 11596 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 4438
       17.82 -    35.64: 361
       35.64 -    53.45: 96
       53.45 -    71.27: 38
       71.27 -    89.09: 18
  Dihedral angle restraints: 4951
    sinusoidal: 2303
      harmonic: 2648
  Sorted by residual:
  dihedral pdb=" CA  THR A 351 "
           pdb=" C   THR A 351 "
           pdb=" N   GLY A 352 "
           pdb=" CA  GLY A 352 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.81   26.19     0      5.00e+00 4.00e-02 2.74e+01
  dihedral pdb=" CA  GLY B 273 "
           pdb=" C   GLY B 273 "
           pdb=" N   ILE B 274 "
           pdb=" CA  ILE B 274 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.61   25.39     0      5.00e+00 4.00e-02 2.58e+01
  dihedral pdb=" CA  ASP A 237 "
           pdb=" C   ASP A 237 "
           pdb=" N   LYS A 238 "
           pdb=" CA  LYS A 238 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.87  -24.13     0      5.00e+00 4.00e-02 2.33e+01
  ... (remaining 4948 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 853
       0.057 -    0.113: 333
       0.113 -    0.169: 65
       0.169 -    0.226: 15
       0.226 -    0.282: 7
  Chirality restraints: 1273
  Sorted by residual:
  chirality pdb=" C3'  DG F  31 "
            pdb=" C4'  DG F  31 "
            pdb=" O3'  DG F  31 "
            pdb=" C2'  DG F  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.45   -0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" C3'  DG F  32 "
            pdb=" C4'  DG F  32 "
            pdb=" O3'  DG F  32 "
            pdb=" C2'  DG F  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.47   -0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" C3'  DG F  12 "
            pdb=" C4'  DG F  12 "
            pdb=" O3'  DG F  12 "
            pdb=" C2'  DG F  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.48   -0.25 2.00e-01 2.50e+01 1.57e+00
  ... (remaining 1270 not shown)

  Planarity restraints: 1333
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC F   1 "   -0.152 2.00e-02 2.50e+03   7.67e-02 1.33e+02
        pdb=" N1   DC F   1 "    0.016 2.00e-02 2.50e+03
        pdb=" C2   DC F   1 "    0.032 2.00e-02 2.50e+03
        pdb=" O2   DC F   1 "    0.083 2.00e-02 2.50e+03
        pdb=" N3   DC F   1 "   -0.022 2.00e-02 2.50e+03
        pdb=" C4   DC F   1 "   -0.008 2.00e-02 2.50e+03
        pdb=" N4   DC F   1 "   -0.099 2.00e-02 2.50e+03
        pdb=" C5   DC F   1 "    0.071 2.00e-02 2.50e+03
        pdb=" C6   DC F   1 "    0.080 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' OMC F   4 "   -0.091 2.00e-02 2.50e+03   5.26e-02 6.22e+01
        pdb=" N1  OMC F   4 "   -0.008 2.00e-02 2.50e+03
        pdb=" C2  OMC F   4 "   -0.010 2.00e-02 2.50e+03
        pdb=" O2  OMC F   4 "    0.081 2.00e-02 2.50e+03
        pdb=" N3  OMC F   4 "   -0.019 2.00e-02 2.50e+03
        pdb=" C4  OMC F   4 "   -0.025 2.00e-02 2.50e+03
        pdb=" N4  OMC F   4 "   -0.045 2.00e-02 2.50e+03
        pdb=" C5  OMC F   4 "    0.049 2.00e-02 2.50e+03
        pdb=" C6  OMC F   4 "    0.067 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' OMC F   2 "   -0.104 2.00e-02 2.50e+03   5.06e-02 5.77e+01
        pdb=" N1  OMC F   2 "    0.020 2.00e-02 2.50e+03
        pdb=" C2  OMC F   2 "    0.013 2.00e-02 2.50e+03
        pdb=" O2  OMC F   2 "    0.057 2.00e-02 2.50e+03
        pdb=" N3  OMC F   2 "   -0.010 2.00e-02 2.50e+03
        pdb=" C4  OMC F   2 "   -0.031 2.00e-02 2.50e+03
        pdb=" N4  OMC F   2 "   -0.041 2.00e-02 2.50e+03
        pdb=" C5  OMC F   2 "    0.024 2.00e-02 2.50e+03
        pdb=" C6  OMC F   2 "    0.071 2.00e-02 2.50e+03
  ... (remaining 1330 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.19: 3
        2.19 -     2.87: 2688
        2.87 -     3.55: 11703
        3.55 -     4.22: 21697
        4.22 -     4.90: 34837
  Nonbonded interactions: 70928
  Sorted by model distance:
  nonbonded pdb=" OP1  DA F  35 "
            pdb="MG    MG F 101 "
     model   vdw
     1.514 2.170
  nonbonded pdb=" OD1 ASP A 110 "
            pdb="MG    MG F 101 "
     model   vdw
     1.933 2.170
  nonbonded pdb=" OD1 ASP A 185 "
            pdb="MG    MG F 101 "
     model   vdw
     2.126 2.170
  nonbonded pdb=" OD2 ASP A 185 "
            pdb="MG    MG A 602 "
     model   vdw
     2.275 2.170
  nonbonded pdb=" O6  POP A 601 "
            pdb="MG    MG A 602 "
     model   vdw
     2.276 2.170
  ... (remaining 70923 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=0.39 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:             19.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.020
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
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      :  0.007   0.096   8423  Z= 0.449
  Angle     :  0.995   7.554  11601  Z= 0.634
  Chirality :  0.063   0.282   1273
  Planarity :  0.009   0.102   1333
  Dihedral  : 15.742  89.088   3239
  Min Nonbonded Distance : 1.514

Molprobity Statistics.
  All-atom Clashscore : 1.82
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.35 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.25), residues: 893
  helix: -0.81 (0.25), residues: 308
  sheet: -0.30 (0.37), residues: 158
  loop : -0.47 (0.27), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.002   ARG A 211 
 TYR   0.050   0.007   TYR A 181 
 PHE   0.027   0.004   PHE B 416 
 TRP   0.048   0.005   TRP A 212 
 HIS   0.011   0.003   HIS B 208 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00709 /  0.45 ( 8423)
  covalent geometry    : angle       0.99516 /  0.63 (11601)
  hydrogen bonds       : bond        0.13453 /  8.99 (  377)
  hydrogen bonds       : angle       6.30895 /  4.49 (  991)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.6914
  time to fit residues: 114.5500
Evaluate side-chains
  89 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74]
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.1980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 373 GLN
A 428 GLN
A 509 GLN
B 137 ASN
** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 278 GLN
B 336 GLN
B 343 GLN
B 373 GLN
B 407 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.118439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.093382 restraints weight = 12066.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 2.03
r_work: 0.3168 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3066
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3067
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8423  Z= 0.184
  Angle     :  0.660   8.380  11601  Z= 0.359
  Chirality :  0.047   0.242   1273
  Planarity :  0.004   0.035   1333
  Dihedral  : 15.240  59.845   1339
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  8.89 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.27), residues: 893
  helix:  1.65 (0.29), residues: 303
  sheet:  0.18 (0.36), residues: 173
  loop :  0.18 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  72 
 TYR   0.014   0.002   TYR B 405 
 PHE   0.022   0.002   PHE B 416 
 TRP   0.021   0.002   TRP A  88 
 HIS   0.003   0.001   HIS A 315 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00402 /  0.18 ( 8423)
  covalent geometry    : angle       0.66041 /  0.36 (11601)
  hydrogen bonds       : bond        0.05079 /  3.45 (  377)
  hydrogen bonds       : angle       4.82996 /  3.39 (  991)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8311 (mp0)
REVERT: A  169 GLU cc_start: 0.7861 (tp30) cc_final: 0.7535 (mt-10)
REVERT: A  173 LYS cc_start: 0.8642 (tttm) cc_final: 0.8052 (mppt)
REVERT: A  356 ARG cc_start: 0.8732 (ttt180) cc_final: 0.8377 (ttt90)
REVERT: A  516 GLU cc_start: 0.6816 (tp30) cc_final: 0.6462 (tp30)
REVERT: B  175 ASN cc_start: 0.7551 (m110) cc_final: 0.7128 (m110)
  outliers start: 9
  outliers final: 5
  residues processed: 100
  average time/residue: 0.6246
  time to fit residues: 65.9168
Evaluate side-chains
  91 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  344 GLU
Chi-restraints excluded: chain B residue  379 SER
Chi-restraints excluded: chain B residue  386 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks: [30, 86, 91, 87, 45, 15, 26, 28, 19, 35, 66]
   chunk 30 optimal weight:    0.8980
   chunk 86 optimal weight:    0.5980
   chunk 91 optimal weight:    5.9990
   chunk 87 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 26 optimal weight:    0.3980
   chunk 28 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 428 GLN
A 500 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.117898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.092839 restraints weight = 11979.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.01
r_work: 0.3165 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3064
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   8423  Z= 0.174
  Angle     :  0.597   7.892  11601  Z= 0.324
  Chirality :  0.046   0.190   1273
  Planarity :  0.004   0.034   1333
  Dihedral  : 15.250  59.735   1339
  Min Nonbonded Distance : 1.795

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  :  9.51 %
    Favored  : 88.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.35 (0.28), residues: 893
  helix:  2.28 (0.30), residues: 303
  sheet:  0.12 (0.35), residues: 175
  loop :  0.30 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  72 
 TYR   0.011   0.001   TYR B 144 
 PHE   0.018   0.002   PHE B 416 
 TRP   0.018   0.002   TRP A  88 
 HIS   0.004   0.001   HIS A 208 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.17 ( 8423)
  covalent geometry    : angle       0.59697 /  0.32 (11601)
  hydrogen bonds       : bond        0.04484 /  3.01 (  377)
  hydrogen bonds       : angle       4.57152 /  3.21 (  991)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 GLU cc_start: 0.7865 (tp30) cc_final: 0.7520 (mt-10)
REVERT: A  173 LYS cc_start: 0.8651 (tttm) cc_final: 0.8087 (mppt)
REVERT: A  463 ARG cc_start: 0.8106 (mtp85) cc_final: 0.7701 (mtp180)
REVERT: A  516 GLU cc_start: 0.6790 (tp30) cc_final: 0.6363 (tp30)
REVERT: B   22 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8977 (mtmm)
REVERT: B  123 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8532 (t0)
REVERT: B  175 ASN cc_start: 0.7675 (m110) cc_final: 0.7227 (m110)
REVERT: B  194 GLU cc_start: 0.8014 (mp0) cc_final: 0.7701 (mp0)
REVERT: B  197 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8299 (mt0)
  outliers start: 18
  outliers final: 7
  residues processed: 98
  average time/residue: 0.6569
  time to fit residues: 67.7578
Evaluate side-chains
  93 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain B residue   22 LYS
Chi-restraints excluded: chain B residue  123 ASP
Chi-restraints excluded: chain B residue  197 GLN
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  344 GLU
Chi-restraints excluded: chain B residue  379 SER
Chi-restraints excluded: chain B residue  386 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks: [9, 24, 47, 80, 46, 49, 56, 30, 66, 19, 65]
   chunk 9 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 80 optimal weight:    5.9990
   chunk 46 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 65 optimal weight:    0.1980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 428 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.118075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.093150 restraints weight = 12149.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 2.03
r_work: 0.3174 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (20 function evaluations)
r_final: 0.3074
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8423  Z= 0.162
  Angle     :  0.566   7.936  11601  Z= 0.305
  Chirality :  0.044   0.184   1273
  Planarity :  0.004   0.036   1333
  Dihedral  : 15.116  58.608   1339
  Min Nonbonded Distance : 1.794

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 10.25 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.43 (0.28), residues: 893
  helix:  2.42 (0.30), residues: 303
  sheet:  0.02 (0.34), residues: 180
  loop :  0.37 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  72 
 TYR   0.010   0.001   TYR B 144 
 PHE   0.020   0.002   PHE B 171 
 TRP   0.016   0.001   TRP A  88 
 HIS   0.003   0.001   HIS A 208 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.16 ( 8423)
  covalent geometry    : angle       0.56585 /  0.30 (11601)
  hydrogen bonds       : bond        0.04125 /  2.79 (  377)
  hydrogen bonds       : angle       4.47828 /  3.14 (  991)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  169 GLU cc_start: 0.7926 (tp30) cc_final: 0.7623 (mt-10)
REVERT: A  173 LYS cc_start: 0.8686 (tttm) cc_final: 0.8158 (mppt)
REVERT: A  463 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7850 (mtp180)
REVERT: A  516 GLU cc_start: 0.6820 (tp30) cc_final: 0.6305 (tp30)
REVERT: B   74 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8927 (tp)
REVERT: B  105 SER cc_start: 0.7349 (m) cc_final: 0.7094 (t)
REVERT: B  175 ASN cc_start: 0.7773 (m110) cc_final: 0.7341 (m110)
REVERT: B  194 GLU cc_start: 0.8048 (mp0) cc_final: 0.7748 (mp0)
REVERT: B  197 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8394 (mt0)
REVERT: B  407 GLN cc_start: 0.8731 (mt0) cc_final: 0.8528 (mm110)
  outliers start: 15
  outliers final: 9
  residues processed: 96
  average time/residue: 0.6421
  time to fit residues: 64.9146
Evaluate side-chains
  94 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  197 GLN
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  344 GLU
Chi-restraints excluded: chain B residue  379 SER
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  397 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks: [16, 41, 4, 60, 87, 8, 48, 91, 51, 10, 62]
   chunk 16 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 48 optimal weight:    0.3980
   chunk 91 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 428 GLN
A 487 GLN
A 500 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.117553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.092614 restraints weight = 11998.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 2.02
r_work: 0.3169 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3070
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3070
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8423  Z= 0.168
  Angle     :  0.559   8.064  11601  Z= 0.302
  Chirality :  0.044   0.186   1273
  Planarity :  0.004   0.038   1333
  Dihedral  : 15.049  59.213   1339
  Min Nonbonded Distance : 1.790

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 10.25 %
    Favored  : 87.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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 (0.28), residues: 893
  helix:  2.45 (0.30), residues: 303
  sheet:  0.09 (0.34), residues: 180
  loop :  0.38 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  72 
 TYR   0.010   0.001   TYR B 144 
 PHE   0.020   0.002   PHE B 171 
 TRP   0.016   0.002   TRP A  88 
 HIS   0.004   0.001   HIS A 208 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.17 ( 8423)
  covalent geometry    : angle       0.55898 /  0.30 (11601)
  hydrogen bonds       : bond        0.04101 /  2.77 (  377)
  hydrogen bonds       : angle       4.43725 /  3.11 (  991)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A  169 GLU cc_start: 0.7883 (tp30) cc_final: 0.7413 (mt-10)
REVERT: A  463 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7898 (mtp180)
REVERT: A  516 GLU cc_start: 0.6792 (tp30) cc_final: 0.6255 (tp30)
REVERT: B   74 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8947 (tp)
REVERT: B  105 SER cc_start: 0.7367 (m) cc_final: 0.7114 (t)
REVERT: B  175 ASN cc_start: 0.7795 (m110) cc_final: 0.7374 (m110)
REVERT: B  194 GLU cc_start: 0.8046 (mp0) cc_final: 0.7769 (mp0)
REVERT: B  197 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8414 (mt0)
REVERT: B  281 LYS cc_start: 0.8150 (mttt) cc_final: 0.7835 (mttt)
  outliers start: 20
  outliers final: 11
  residues processed: 96
  average time/residue: 0.6503
  time to fit residues: 65.6846
Evaluate side-chains
  93 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  197 GLN
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  344 GLU
Chi-restraints excluded: chain B residue  379 SER
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  419 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks: [62, 41, 10, 69, 8, 22, 52, 66, 15, 80, 88]
   chunk 62 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0870
   chunk 15 optimal weight:    0.8980
   chunk 80 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.9360

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 428 GLN
A 500 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.116433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.091431 restraints weight = 11946.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 2.01
r_work: 0.3153 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3052
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (12 function evaluations)
r_final: 0.3052
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8706
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8423  Z= 0.203
  Angle     :  0.585   7.366  11601  Z= 0.313
  Chirality :  0.045   0.212   1273
  Planarity :  0.004   0.038   1333
  Dihedral  : 15.114  59.615   1339
  Min Nonbonded Distance : 1.780

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 10.49 %
    Favored  : 87.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.38 (0.28), residues: 893
  helix:  2.28 (0.30), residues: 309
  sheet:  0.11 (0.34), residues: 180
  loop :  0.33 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  72 
 TYR   0.010   0.002   TYR B 144 
 PHE   0.023   0.002   PHE B 171 
 TRP   0.018   0.002   TRP A  88 
 HIS   0.004   0.001   HIS A 208 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00452 /  0.20 ( 8423)
  covalent geometry    : angle       0.58475 /  0.31 (11601)
  hydrogen bonds       : bond        0.04364 /  2.95 (  377)
  hydrogen bonds       : angle       4.49908 /  3.16 (  991)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  169 GLU cc_start: 0.7895 (tp30) cc_final: 0.7431 (mt-10)
REVERT: A  463 ARG cc_start: 0.8238 (mtp85) cc_final: 0.7894 (mtp180)
REVERT: A  516 GLU cc_start: 0.6839 (tp30) cc_final: 0.6310 (tp30)
REVERT: B   74 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8957 (tp)
REVERT: B  105 SER cc_start: 0.7407 (m) cc_final: 0.7144 (t)
REVERT: B  123 ASP cc_start: 0.8763 (t70) cc_final: 0.8492 (t0)
REVERT: B  175 ASN cc_start: 0.7845 (m110) cc_final: 0.7480 (m110)
  outliers start: 19
  outliers final: 14
  residues processed: 92
  average time/residue: 0.6276
  time to fit residues: 60.9008
Evaluate side-chains
  95 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  428 GLN
Chi-restraints excluded: chain A residue  448 ARG
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  344 GLU
Chi-restraints excluded: chain B residue  379 SER
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  419 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks: [10, 76, 89, 70, 22, 51, 17, 75, 0, 15, 29]
   chunk 10 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0970
   chunk 89 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 75 optimal weight:    0.4980
   chunk 0 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 428 GLN
A 500 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.117422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.092206 restraints weight = 12015.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.04
r_work: 0.3160 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3058
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3058
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8423  Z= 0.171
  Angle     :  0.569   7.501  11601  Z= 0.305
  Chirality :  0.044   0.192   1273
  Planarity :  0.004   0.039   1333
  Dihedral  : 15.087  59.685   1339
  Min Nonbonded Distance : 1.791

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 10.74 %
    Favored  : 87.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.40 (0.28), residues: 893
  helix:  2.30 (0.30), residues: 309
  sheet:  0.12 (0.34), residues: 180
  loop :  0.34 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  72 
 TYR   0.013   0.002   TYR A 483 
 PHE   0.025   0.002   PHE B 171 
 TRP   0.017   0.001   TRP A  88 
 HIS   0.003   0.001   HIS A 208 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.17 ( 8423)
  covalent geometry    : angle       0.56871 /  0.30 (11601)
  hydrogen bonds       : bond        0.04125 /  2.79 (  377)
  hydrogen bonds       : angle       4.44666 /  3.12 (  991)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A  169 GLU cc_start: 0.7778 (tp30) cc_final: 0.7487 (mt-10)
REVERT: A  173 LYS cc_start: 0.8580 (tttm) cc_final: 0.8022 (mppt)
REVERT: A  463 ARG cc_start: 0.8129 (mtp85) cc_final: 0.7779 (mtp180)
REVERT: A  516 GLU cc_start: 0.6704 (tp30) cc_final: 0.6193 (tp30)
REVERT: B   74 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8909 (tp)
REVERT: B  105 SER cc_start: 0.7291 (m) cc_final: 0.7021 (t)
REVERT: B  123 ASP cc_start: 0.8764 (t70) cc_final: 0.8492 (t0)
REVERT: B  175 ASN cc_start: 0.7701 (m110) cc_final: 0.7304 (m110)
REVERT: B  194 GLU cc_start: 0.8004 (mp0) cc_final: 0.7323 (pm20)
REVERT: B  197 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7998 (mt0)
  outliers start: 17
  outliers final: 14
  residues processed: 92
  average time/residue: 0.6462
  time to fit residues: 62.8322
Evaluate side-chains
  97 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  428 GLN
Chi-restraints excluded: chain A residue  448 ARG
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  197 GLN
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  344 GLU
Chi-restraints excluded: chain B residue  379 SER
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  419 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks: [52, 53, 40, 33, 87, 28, 80, 32, 0, 90, 82]
   chunk 52 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0270
   chunk 40 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 87 optimal weight:    0.4980
   chunk 28 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 82 optimal weight:    0.5980
   overall best weight:    0.6238

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 428 GLN
A 500 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.117605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.092418 restraints weight = 11933.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 2.04
r_work: 0.3168 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3064
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8423  Z= 0.161
  Angle     :  0.557   7.666  11601  Z= 0.299
  Chirality :  0.044   0.186   1273
  Planarity :  0.004   0.039   1333
  Dihedral  : 15.043  59.795   1339
  Min Nonbonded Distance : 1.797

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 10.49 %
    Favored  : 87.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.43 (0.28), residues: 893
  helix:  2.33 (0.30), residues: 309
  sheet:  0.14 (0.34), residues: 180
  loop :  0.35 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  72 
 TYR   0.010   0.001   TYR B 144 
 PHE   0.027   0.002   PHE B 171 
 TRP   0.017   0.001   TRP A  88 
 HIS   0.003   0.001   HIS A 208 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.16 ( 8423)
  covalent geometry    : angle       0.55691 /  0.30 (11601)
  hydrogen bonds       : bond        0.04017 /  2.72 (  377)
  hydrogen bonds       : angle       4.41199 /  3.10 (  991)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A  169 GLU cc_start: 0.7765 (tp30) cc_final: 0.7487 (mt-10)
REVERT: A  173 LYS cc_start: 0.8574 (tttm) cc_final: 0.8030 (mppt)
REVERT: A  463 ARG cc_start: 0.8138 (mtp85) cc_final: 0.7799 (mtp180)
REVERT: A  516 GLU cc_start: 0.6672 (tp30) cc_final: 0.6167 (tp30)
REVERT: B   74 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8913 (tp)
REVERT: B  105 SER cc_start: 0.7280 (m) cc_final: 0.7026 (t)
REVERT: B  123 ASP cc_start: 0.8765 (t70) cc_final: 0.8489 (t0)
REVERT: B  175 ASN cc_start: 0.7705 (m110) cc_final: 0.7306 (m110)
REVERT: B  194 GLU cc_start: 0.7973 (mp0) cc_final: 0.7292 (pm20)
REVERT: B  197 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8009 (mt0)
  outliers start: 19
  outliers final: 14
  residues processed: 92
  average time/residue: 0.6413
  time to fit residues: 62.3522
Evaluate side-chains
  97 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  428 GLN
Chi-restraints excluded: chain A residue  448 ARG
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  197 GLN
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  344 GLU
Chi-restraints excluded: chain B residue  379 SER
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  419 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks: [83, 61, 62, 8, 68, 91, 32, 82, 74, 86, 5]
   chunk 83 optimal weight:    0.0670
   chunk 61 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 82 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0970
   chunk 86 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0370
   overall best weight:    0.3394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 428 GLN
A 500 GLN
B 147 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.118935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.093950 restraints weight = 11962.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 2.03
r_work: 0.3194 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8423  Z= 0.128
  Angle     :  0.535   8.578  11601  Z= 0.287
  Chirality :  0.043   0.176   1273
  Planarity :  0.003   0.039   1333
  Dihedral  : 14.944  59.846   1339
  Min Nonbonded Distance : 1.810

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 11.23 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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 (0.28), residues: 893
  helix:  2.42 (0.30), residues: 309
  sheet:  0.21 (0.35), residues: 174
  loop :  0.35 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  72 
 TYR   0.012   0.001   TYR A 427 
 PHE   0.027   0.002   PHE B 171 
 TRP   0.016   0.001   TRP A  88 
 HIS   0.002   0.001   HIS A 208 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.13 ( 8423)
  covalent geometry    : angle       0.53485 /  0.29 (11601)
  hydrogen bonds       : bond        0.03668 /  2.49 (  377)
  hydrogen bonds       : angle       4.32382 /  3.03 (  991)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A  169 GLU cc_start: 0.7755 (tp30) cc_final: 0.7483 (mt-10)
REVERT: A  173 LYS cc_start: 0.8569 (tttm) cc_final: 0.8032 (mppt)
REVERT: A  463 ARG cc_start: 0.8149 (mtp85) cc_final: 0.7826 (mtp180)
REVERT: A  516 GLU cc_start: 0.6676 (tp30) cc_final: 0.6182 (tp30)
REVERT: B  105 SER cc_start: 0.7217 (m) cc_final: 0.7000 (t)
REVERT: B  123 ASP cc_start: 0.8747 (t70) cc_final: 0.8469 (t0)
REVERT: B  175 ASN cc_start: 0.7706 (m110) cc_final: 0.7309 (m110)
REVERT: B  194 GLU cc_start: 0.7960 (mp0) cc_final: 0.7293 (pm20)
REVERT: B  197 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8017 (mt0)
  outliers start: 15
  outliers final: 11
  residues processed: 93
  average time/residue: 0.6376
  time to fit residues: 62.6160
Evaluate side-chains
  92 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  448 ARG
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue  197 GLN
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  379 SER
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  419 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks: [61, 47, 16, 57, 85, 65, 30, 20, 76, 13, 17]
   chunk 61 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0970
   chunk 30 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.5578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 428 GLN
A 500 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.118314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.093177 restraints weight = 11881.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 2.04
r_work: 0.3180 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3078
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3078
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.2728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8423  Z= 0.149
  Angle     :  0.542   8.452  11601  Z= 0.290
  Chirality :  0.043   0.177   1273
  Planarity :  0.003   0.039   1333
  Dihedral  : 14.930  59.930   1339
  Min Nonbonded Distance : 1.802

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 11.11 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.53 (0.28), residues: 893
  helix:  2.40 (0.30), residues: 309
  sheet:  0.21 (0.35), residues: 180
  loop :  0.42 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  72 
 TYR   0.010   0.001   TYR B 144 
 PHE   0.028   0.002   PHE B 171 
 TRP   0.016   0.001   TRP A  88 
 HIS   0.003   0.001   HIS A 208 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.15 ( 8423)
  covalent geometry    : angle       0.54206 /  0.29 (11601)
  hydrogen bonds       : bond        0.03829 /  2.59 (  377)
  hydrogen bonds       : angle       4.34676 /  3.05 (  991)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A  169 GLU cc_start: 0.7753 (tp30) cc_final: 0.7536 (mt-10)
REVERT: A  173 LYS cc_start: 0.8559 (tttm) cc_final: 0.8026 (mppt)
REVERT: A  463 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7846 (mtp180)
REVERT: B  105 SER cc_start: 0.7210 (m) cc_final: 0.7000 (t)
REVERT: B  123 ASP cc_start: 0.8746 (t70) cc_final: 0.8473 (t0)
REVERT: B  175 ASN cc_start: 0.7675 (m110) cc_final: 0.7293 (m110)
REVERT: B  194 GLU cc_start: 0.7963 (mp0) cc_final: 0.7296 (pm20)
REVERT: B  197 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8013 (mt0)
  outliers start: 15
  outliers final: 11
  residues processed: 91
  average time/residue: 0.6157
  time to fit residues: 59.4186
Evaluate side-chains
  90 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  448 ARG
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue  197 GLN
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  379 SER
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  419 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks: [53, 68, 20, 8, 67, 78, 36, 26, 46, 4, 5]
   chunk 53 optimal weight:    0.4980
   chunk 68 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0570
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 174 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.118225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.093071 restraints weight = 11906.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 2.05
r_work: 0.3177 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3076
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3076 r_free = 0.3076    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3076 r_free = 0.3076    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3076
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8423  Z= 0.151
  Angle     :  0.551   8.356  11601  Z= 0.294
  Chirality :  0.043   0.176   1273
  Planarity :  0.004   0.048   1333
  Dihedral  : 14.943  59.769   1339
  Min Nonbonded Distance : 1.800

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 11.85 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.56 (0.28), residues: 893
  helix:  2.40 (0.30), residues: 309
  sheet:  0.24 (0.35), residues: 180
  loop :  0.45 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 358 
 TYR   0.011   0.001   TYR A 483 
 PHE   0.029   0.002   PHE B 171 
 TRP   0.016   0.001   TRP A  88 
 HIS   0.003   0.001   HIS A 208 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.15 ( 8423)
  covalent geometry    : angle       0.55093 /  0.29 (11601)
  hydrogen bonds       : bond        0.03833 /  2.60 (  377)
  hydrogen bonds       : angle       4.34731 /  3.05 (  991)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5427.80 seconds
wall clock time: 92 minutes 55.02 seconds (5575.02 seconds total)