Starting phenix.real_space_refine
on Thu Jul  2 02:31:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rao_19021/07_2026/8rao_19021.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rao_19021/07_2026/8rao_19021.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rao_19021/07_2026/8rao_19021.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rao_19021/07_2026/8rao_19021.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rao_19021/07_2026/8rao_19021.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rao_19021/07_2026/8rao_19021.cif"
  }
  resolution = 4.4
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 8
    Type Number    sf(0)   Gaussians
     P      11      5.49       5
     Mg      1      5.21       5
     S      31      5.16       5
     Be      1      3.05       5
     C    3604      2.51       5
     N    1010      2.21       5
     O    1120      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5781
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "O"
      Number of atoms: 5557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 694, 5557
          Classifications: {'peptide': 694}
          Link IDs: {'PTRANS': 28, 'TRANS': 665}
          Chain breaks: 2
    Chain: "P"
      Number of atoms: 192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 192
          Classifications: {'RNA': 9}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 1, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 4, 'rna3p': 4}
    Chain: "O"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.47, per 1000 atoms: 0.25
  Number of scatterers: 5781
  At special positions: 0
  Unit cell: (77.7, 102.9, 96.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      31     16.00
     P      11     15.00
     Mg      1     11.99
     F       3      9.00
     O    1120      8.00
     N    1010      7.00
     C    3604      6.00
     Be      1      4.00
    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: 0.57
  Conformation dependent library (CDL) restraints added in 333.7 milliseconds
  

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1312

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 4 sheets defined
      52.9% alpha, 15.6% beta
      0 base pairs and 2 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'O' and resid 1095 through 1110
    Processing helix  chain 'O' and resid 1113 through 1121
    Processing helix  chain 'O' and resid 1136 through 1140
    Processing helix  chain 'O' and resid 1149 through 1175
      Proline residue:  O1159  - end of helix
    Processing helix  chain 'O' and resid 1203 through 1210
    Processing helix  chain 'O' and resid 1232 through 1239
      removed outlier: 3.629A  pdb=" N   PHE O1236 " --> pdb=" O   SER O1232 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1268 through 1274
    Processing helix  chain 'O' and resid 1288 through 1301
    Processing helix  chain 'O' and resid 1302 through 1305
      removed outlier: 6.161A  pdb=" N   ASP O1305 " --> pdb=" O   GLU O1302 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 1302 through 1305'
    Processing helix  chain 'O' and resid 1306 through 1313
    Processing helix  chain 'O' and resid 1322 through 1334
      removed outlier: 3.616A  pdb=" N   ILE O1326 " --> pdb=" O   ASP O1322 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1336 through 1349
    Processing helix  chain 'O' and resid 1362 through 1377
    Processing helix  chain 'O' and resid 1412 through 1425
      removed outlier: 3.617A  pdb=" N   SER O1425 " --> pdb=" O   LEU O1421 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1452 through 1455
    Processing helix  chain 'O' and resid 1456 through 1465
    Processing helix  chain 'O' and resid 1531 through 1562
    Processing helix  chain 'O' and resid 1570 through 1573
      removed outlier: 3.702A  pdb=" N   ALA O1573 " --> pdb=" O   SER O1570 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 1570 through 1573'
    Processing helix  chain 'O' and resid 1574 through 1581
    Processing helix  chain 'O' and resid 1592 through 1595
      removed outlier: 3.589A  pdb=" N   CYS O1595 " --> pdb=" O   ALA O1592 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 1592 through 1595'
    Processing helix  chain 'O' and resid 1596 through 1602
    Processing helix  chain 'O' and resid 1603 through 1606
      removed outlier: 3.819A  pdb=" N   TYR O1606 " --> pdb=" O   PRO O1603 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 1603 through 1606'
    Processing helix  chain 'O' and resid 1626 through 1632
    Processing helix  chain 'O' and resid 1637 through 1646
    Processing helix  chain 'O' and resid 1658 through 1669
      removed outlier: 4.550A  pdb=" N   PHE O1664 " --> pdb=" O   SER O1660 " (cutoff:3.500A)
      Proline residue:  O1665  - end of helix
    Processing helix  chain 'O' and resid 1679 through 1684
    Processing helix  chain 'O' and resid 1686 through 1691
      removed outlier: 4.041A  pdb=" N   GLN O1690 " --> pdb=" O   ARG O1686 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   LEU O1691 " --> pdb=" O   PRO O1687 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 1686 through 1691'
    Processing helix  chain 'O' and resid 1718 through 1737
      removed outlier: 3.955A  pdb=" N   ILE O1722 " --> pdb=" O   ASN O1718 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1752 through 1767
    Processing helix  chain 'O' and resid 1769 through 1774
      removed outlier: 3.996A  pdb=" N   LYS O1773 " --> pdb=" O   GLY O1769 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1805 through 1809
      removed outlier: 3.873A  pdb=" N   LEU O1808 " --> pdb=" O   VAL O1805 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1810 through 1819
      removed outlier: 3.606A  pdb=" N   MET O1814 " --> pdb=" O   ASP O1810 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1830 through 1836
      removed outlier: 3.871A  pdb=" N   LYS O1836 " --> pdb=" O   ARG O1832 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1837 through 1850
    Processing helix  chain 'O' and resid 1865 through 1876
      removed outlier: 3.783A  pdb=" N   GLN O1869 " --> pdb=" O   ASN O1865 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'O' and resid 1188 through 1191
      removed outlier: 3.655A  pdb=" N   ASN O1257 " --> pdb=" O   THR O1253 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   THR O1249 " --> pdb=" O   THR O1261 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   ARG O1263 " --> pdb=" O   VAL O1247 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   VAL O1247 " --> pdb=" O   ARG O1263 " (cutoff:3.500A)
      removed outlier: 8.635A  pdb=" N   HIS O1265 " --> pdb=" O   ALA O1245 " (cutoff:3.500A)
      removed outlier: 8.886A  pdb=" N   ALA O1245 " --> pdb=" O   HIS O1265 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   ASP O1215 " --> pdb=" O   VAL O1247 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   LEU O1216 " --> pdb=" O   VAL O1285 " (cutoff:3.500A)
      removed outlier: 8.867A  pdb=" N   SER O1182 " --> pdb=" O   ALA O1202 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   ALA O1202 " --> pdb=" O   SER O1182 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ILE O1184 " --> pdb=" O   SER O1200 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   SER O1200 " --> pdb=" O   ILE O1184 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'O' and resid 1439 through 1441
      removed outlier: 6.606A  pdb=" N   ILE O1406 " --> pdb=" O   ILE O1565 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   SER O1567 " --> pdb=" O   ILE O1406 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   ILE O1408 " --> pdb=" O   SER O1567 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   VAL O1587 " --> pdb=" O   ILE O1612 " (cutoff:3.500A)
      removed outlier: 7.941A  pdb=" N   VAL O1614 " --> pdb=" O   VAL O1587 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   ILE O1589 " --> pdb=" O   VAL O1614 " (cutoff:3.500A)
      removed outlier: 5.814A  pdb=" N   GLY O1351 " --> pdb=" O   CYS O1611 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   MET O1613 " --> pdb=" O   GLY O1351 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   SER O1353 " --> pdb=" O   MET O1613 " (cutoff:3.500A)
      removed outlier: 8.791A  pdb=" N   TYR O1649 " --> pdb=" O   PHE O1352 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   LEU O1354 " --> pdb=" O   TYR O1649 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'O' and resid 1427 through 1428
    Processing sheet with id=AA4, first strand: chain 'O' and resid 1775 through 1778
      removed outlier: 6.779A  pdb=" N   ILE O1746 " --> pdb=" O   ASP O1776 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   ASN O1778 " --> pdb=" O   ILE O1746 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   ILE O1748 " --> pdb=" O   ASN O1778 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   GLY O1747 " --> pdb=" O   LEU O1792 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   SER O1794 " --> pdb=" O   GLY O1747 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ILE O1749 " --> pdb=" O   SER O1794 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   GLU O1789 " --> pdb=" O   SER O1824 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   TRP O1826 " --> pdb=" O   GLU O1789 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   ILE O1791 " --> pdb=" O   TRP O1826 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   LEU O1828 " --> pdb=" O   ILE O1791 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ILE O1793 " --> pdb=" O   LEU O1828 " (cutoff:3.500A)
      removed outlier: 7.956A  pdb=" N   ALA O1854 " --> pdb=" O   TYR O1697 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   PHE O1699 " --> pdb=" O   ALA O1854 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   ALA O1856 " --> pdb=" O   PHE O1699 " (cutoff:3.500A)
      removed outlier: 5.285A  pdb=" N   ASP O1701 " --> pdb=" O   ALA O1856 " (cutoff:3.500A)

    256 hydrogen bonds defined for protein.
    735 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      2 stacking parallelities
  Total time for adding SS restraints: 0.94

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1854
        1.34 -     1.45: 742
        1.45 -     1.57: 3239
        1.57 -     1.69: 20
        1.69 -     1.81: 49
  Bond restraints: 5904
  Sorted by residual:
  bond pdb=" F2  BEF O3003 "
       pdb="BE   BEF O3003 "
    ideal  model  delta    sigma   weight residual
    1.476  1.562 -0.086 2.00e-02 2.50e+03 1.83e+01
  bond pdb=" F3  BEF O3003 "
       pdb="BE   BEF O3003 "
    ideal  model  delta    sigma   weight residual
    1.476  1.546 -0.070 2.00e-02 2.50e+03 1.22e+01
  bond pdb=" F1  BEF O3003 "
       pdb="BE   BEF O3003 "
    ideal  model  delta    sigma   weight residual
    1.476  1.534 -0.058 2.00e-02 2.50e+03 8.42e+00
  bond pdb=" N1    C P   4 "
       pdb=" C2    C P   4 "
    ideal  model  delta    sigma   weight residual
    1.397  1.410 -0.013 1.00e-02 1.00e+04 1.58e+00
  bond pdb=" C4  ADP O3001 "
       pdb=" C5  ADP O3001 "
    ideal  model  delta    sigma   weight residual
    1.490  1.470  0.020 2.00e-02 2.50e+03 1.02e+00
  ... (remaining 5899 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 7953
        2.52 -     5.04: 41
        5.04 -     7.55: 6
        7.55 -    10.07: 0
       10.07 -    12.59: 2
  Bond angle restraints: 8002
  Sorted by residual:
  angle pdb=" C1'   C P   4 "
        pdb=" N1    C P   4 "
        pdb=" C2    C P   4 "
      ideal   model   delta    sigma   weight residual
     118.80  125.43   -6.63 1.10e+00 8.26e-01 3.63e+01
  angle pdb=" N1    C P   4 "
        pdb=" C2    C P   4 "
        pdb=" O2    C P   4 "
      ideal   model   delta    sigma   weight residual
     118.90  121.89   -2.99 6.00e-01 2.78e+00 2.48e+01
  angle pdb=" C1'   C P   4 "
        pdb=" N1    C P   4 "
        pdb=" C6    C P   4 "
      ideal   model   delta    sigma   weight residual
     120.80  115.60    5.20 1.20e+00 6.94e-01 1.88e+01
  angle pdb=" F2  BEF O3003 "
        pdb="BE   BEF O3003 "
        pdb=" F3  BEF O3003 "
      ideal   model   delta    sigma   weight residual
     119.96  107.37   12.59 3.00e+00 1.11e-01 1.76e+01
  angle pdb=" O2    C P   4 "
        pdb=" C2    C P   4 "
        pdb=" N3    C P   4 "
      ideal   model   delta    sigma   weight residual
     121.90  118.98    2.92 7.00e-01 2.04e+00 1.74e+01
  ... (remaining 7997 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.90: 3556
       23.90 -    47.80: 57
       47.80 -    71.70: 26
       71.70 -    95.60: 4
       95.60 -   119.51: 2
  Dihedral angle restraints: 3645
    sinusoidal: 1614
      harmonic: 2031
  Sorted by residual:
  dihedral pdb=" O4'   C P   4 "
           pdb=" C1'   C P   4 "
           pdb=" N1    C P   4 "
           pdb=" C2    C P   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00  102.01   97.99     1      1.50e+01 4.44e-03 4.86e+01
  dihedral pdb=" O1B ADP O3001 "
           pdb=" O3A ADP O3001 "
           pdb=" PB  ADP O3001 "
           pdb=" PA  ADP O3001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -179.51  119.51     1      2.00e+01 2.50e-03 3.58e+01
  dihedral pdb=" O5'   C P   8 "
           pdb=" C5'   C P   8 "
           pdb=" C4'   C P   8 "
           pdb=" C3'   C P   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.00  114.85  -59.85     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 3642 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 587
       0.025 -    0.051: 180
       0.051 -    0.076: 45
       0.076 -    0.101: 40
       0.101 -    0.126: 35
  Chirality restraints: 887
  Sorted by residual:
  chirality pdb=" CA  ILE O1280 "
            pdb=" N   ILE O1280 "
            pdb=" C   ILE O1280 "
            pdb=" CB  ILE O1280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.98e-01
  chirality pdb=" CA  ILE O1825 "
            pdb=" N   ILE O1825 "
            pdb=" C   ILE O1825 "
            pdb=" CB  ILE O1825 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.85e-01
  chirality pdb=" CA  ILE O1564 "
            pdb=" N   ILE O1564 "
            pdb=" C   ILE O1564 "
            pdb=" CB  ILE O1564 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  ... (remaining 884 not shown)

  Planarity restraints: 997
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER O1647 "    0.018 5.00e-02 4.00e+02   2.66e-02 1.13e+00
        pdb=" N   PRO O1648 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO O1648 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO O1648 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU O1222 "   -0.014 5.00e-02 4.00e+02   2.19e-02 7.70e-01
        pdb=" N   PRO O1223 "    0.038 5.00e-02 4.00e+02
        pdb=" CA  PRO O1223 "   -0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO O1223 "   -0.012 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY O1357 "    0.013 5.00e-02 4.00e+02   1.97e-02 6.21e-01
        pdb=" N   PRO O1358 "   -0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO O1358 "    0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO O1358 "    0.011 5.00e-02 4.00e+02
  ... (remaining 994 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.59: 59
        2.59 -     3.17: 5264
        3.17 -     3.75: 9127
        3.75 -     4.32: 13028
        4.32 -     4.90: 21362
  Nonbonded interactions: 48840
  Sorted by model distance:
  nonbonded pdb=" OG1 THR O1364 "
            pdb="MG    MG O3002 "
     model   vdw
     2.016 2.170
  nonbonded pdb=" O2B ADP O3001 "
            pdb="MG    MG O3002 "
     model   vdw
     2.016 2.170
  nonbonded pdb=" OE2 GLU O1591 "
            pdb=" F1  BEF O3003 "
     model   vdw
     2.166 2.990
  nonbonded pdb=" O   TYR O1125 "
            pdb=" NH1 ARG O1173 "
     model   vdw
     2.167 3.120
  nonbonded pdb=" OG  SER O1332 "
            pdb=" O   LYS O1430 "
     model   vdw
     2.174 3.040
  ... (remaining 48835 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.580
  Find NCS groups from input model:        0.020
  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:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
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      :  0.002   0.086   5904  Z= 0.118
  Angle     :  0.462  12.589   8002  Z= 0.252
  Chirality :  0.038   0.126    887
  Planarity :  0.002   0.027    997
  Dihedral  : 10.681 119.506   2333
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.69 (0.34), residues: 688
  helix:  3.31 (0.31), residues: 333
  sheet:  0.87 (0.44), residues: 129
  loop : -0.05 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG O1820 
 TYR   0.004   0.000   TYR O1195 
 PHE   0.006   0.001   PHE O1860 
 TRP   0.003   0.000   TRP O1688 
 HIS   0.002   0.000   HIS O1574 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00222 /  0.12 ( 5904)
  covalent geometry    : angle       0.46205 /  0.25 ( 8002)
  hydrogen bonds       : bond        0.13236 /  9.36 (  256)
  hydrogen bonds       : angle       4.24797 /  3.21 (  735)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9440 (tpt) cc_final: 0.9047 (tpt)
REVERT: O 1157 MET cc_start: 0.9183 (mmm) cc_final: 0.8705 (mmm)
REVERT: O 1162 LEU cc_start: 0.9747 (mt) cc_final: 0.9500 (pp)
REVERT: O 1294 GLU cc_start: 0.9405 (mt-10) cc_final: 0.9175 (mt-10)
REVERT: O 1439 LEU cc_start: 0.6606 (tp) cc_final: 0.4435 (tp)
REVERT: O 1566 CYS cc_start: 0.9572 (m) cc_final: 0.9255 (p)
REVERT: O 1582 ILE cc_start: 0.8955 (pt) cc_final: 0.7624 (pt)
REVERT: O 1584 PHE cc_start: 0.9071 (m-80) cc_final: 0.8682 (m-80)
REVERT: O 1613 MET cc_start: 0.9669 (mtm) cc_final: 0.9242 (mtp)
REVERT: O 1625 LEU cc_start: 0.9645 (mt) cc_final: 0.9440 (mm)
REVERT: O 1783 PHE cc_start: 0.9209 (t80) cc_final: 0.8629 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1062
  time to fit residues: 17.5798
Evaluate side-chains
  84 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O1104 HIS
O1139 ASN
O1555 GLN
O1757 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.050945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.036467 restraints weight = 39231.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.037791 restraints weight = 25146.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.038750 restraints weight = 18388.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.039345 restraints weight = 14666.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.039863 restraints weight = 12605.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5904  Z= 0.145
  Angle     :  0.591   7.183   8002  Z= 0.300
  Chirality :  0.043   0.291    887
  Planarity :  0.004   0.041    997
  Dihedral  : 12.912 109.632    925
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.33), residues: 688
  helix:  2.45 (0.30), residues: 339
  sheet:  0.69 (0.43), residues: 130
  loop : -0.03 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG O1610 
 TYR   0.010   0.001   TYR O1117 
 PHE   0.033   0.002   PHE O1763 
 TRP   0.009   0.001   TRP O1166 
 HIS   0.002   0.001   HIS O1268 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.15 ( 5904)
  covalent geometry    : angle       0.59080 /  0.30 ( 8002)
  hydrogen bonds       : bond        0.03646 /  2.40 (  256)
  hydrogen bonds       : angle       4.37291 /  3.25 (  735)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9346 (tpt) cc_final: 0.8891 (tpt)
REVERT: O 1157 MET cc_start: 0.8843 (mmm) cc_final: 0.8484 (mmm)
REVERT: O 1216 LEU cc_start: 0.8974 (tp) cc_final: 0.8621 (tt)
REVERT: O 1418 GLU cc_start: 0.8993 (tt0) cc_final: 0.8690 (mt-10)
REVERT: O 1566 CYS cc_start: 0.9517 (m) cc_final: 0.9277 (p)
REVERT: O 1613 MET cc_start: 0.9564 (mtm) cc_final: 0.8441 (mtm)
REVERT: O 1657 MET cc_start: 0.8170 (mmp) cc_final: 0.7831 (mmp)
REVERT: O 1776 ASP cc_start: 0.8722 (t0) cc_final: 0.8042 (m-30)
REVERT: O 1783 PHE cc_start: 0.9063 (t80) cc_final: 0.8310 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0943
  time to fit residues: 12.5543
Evaluate side-chains
  74 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O1241 HIS
O1312 GLN
O1757 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.049544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.035134 restraints weight = 40310.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.036370 restraints weight = 26266.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.037212 restraints weight = 19492.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.037853 restraints weight = 15792.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.038231 restraints weight = 13587.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5904  Z= 0.160
  Angle     :  0.566   9.440   8002  Z= 0.283
  Chirality :  0.042   0.270    887
  Planarity :  0.004   0.044    997
  Dihedral  : 12.986 113.386    925
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.90 (0.33), residues: 688
  helix:  2.27 (0.29), residues: 338
  sheet:  0.71 (0.42), residues: 132
  loop :  0.09 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG O1641 
 TYR   0.015   0.001   TYR O1195 
 PHE   0.022   0.001   PHE O1763 
 TRP   0.026   0.002   TRP O1840 
 HIS   0.003   0.001   HIS O1574 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.16 ( 5904)
  covalent geometry    : angle       0.56622 /  0.28 ( 8002)
  hydrogen bonds       : bond        0.03265 /  2.12 (  256)
  hydrogen bonds       : angle       4.29849 /  3.16 (  735)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9352 (tpt) cc_final: 0.8919 (tpt)
REVERT: O 1157 MET cc_start: 0.8928 (mmm) cc_final: 0.8538 (mmm)
REVERT: O 1162 LEU cc_start: 0.9779 (mm) cc_final: 0.9431 (pp)
REVERT: O 1192 SER cc_start: 0.8790 (m) cc_final: 0.8266 (p)
REVERT: O 1195 TYR cc_start: 0.7896 (m-10) cc_final: 0.7611 (m-80)
REVERT: O 1286 MET cc_start: 0.8025 (pmm) cc_final: 0.7642 (pmm)
REVERT: O 1294 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8971 (mt-10)
REVERT: O 1421 LEU cc_start: 0.9544 (tp) cc_final: 0.9196 (pp)
REVERT: O 1566 CYS cc_start: 0.9532 (m) cc_final: 0.9055 (p)
REVERT: O 1584 PHE cc_start: 0.9142 (m-10) cc_final: 0.8536 (m-80)
REVERT: O 1613 MET cc_start: 0.9587 (mtm) cc_final: 0.8287 (mtm)
REVERT: O 1642 MET cc_start: 0.9526 (mmp) cc_final: 0.8895 (mmm)
REVERT: O 1657 MET cc_start: 0.8397 (mmp) cc_final: 0.8059 (mmp)
REVERT: O 1680 MET cc_start: 0.8346 (mmm) cc_final: 0.8042 (mmm)
REVERT: O 1760 ARG cc_start: 0.9620 (mtm110) cc_final: 0.9408 (mtm110)
REVERT: O 1776 ASP cc_start: 0.8668 (t0) cc_final: 0.8089 (m-30)
REVERT: O 1783 PHE cc_start: 0.9083 (t80) cc_final: 0.8346 (t80)
REVERT: O 1814 MET cc_start: 0.9534 (mtt) cc_final: 0.8944 (mmm)
REVERT: O 1840 TRP cc_start: 0.9111 (m100) cc_final: 0.8434 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0993
  time to fit residues: 11.3874
Evaluate side-chains
  70 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 25 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0020
   chunk 49 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 43 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    1.1392

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O1241 HIS
O1309 GLN
O1757 GLN
O1831 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.048583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.034166 restraints weight = 40879.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.035373 restraints weight = 26380.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.036244 restraints weight = 19529.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.036803 restraints weight = 15734.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.037234 restraints weight = 13598.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5904  Z= 0.154
  Angle     :  0.542   8.848   8002  Z= 0.273
  Chirality :  0.041   0.306    887
  Planarity :  0.004   0.052    997
  Dihedral  : 13.000 120.177    925
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.33), residues: 688
  helix:  2.15 (0.29), residues: 338
  sheet:  0.73 (0.42), residues: 132
  loop :  0.05 (0.44), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG O1266 
 TYR   0.022   0.001   TYR O1140 
 PHE   0.015   0.001   PHE O1777 
 TRP   0.009   0.001   TRP O1840 
 HIS   0.003   0.001   HIS O1574 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.15 ( 5904)
  covalent geometry    : angle       0.54156 /  0.27 ( 8002)
  hydrogen bonds       : bond        0.02994 /  1.96 (  256)
  hydrogen bonds       : angle       4.35224 /  3.20 (  735)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9315 (tpt) cc_final: 0.8861 (tpt)
REVERT: O 1157 MET cc_start: 0.8926 (mmm) cc_final: 0.8541 (mmm)
REVERT: O 1162 LEU cc_start: 0.9788 (mm) cc_final: 0.9448 (pp)
REVERT: O 1286 MET cc_start: 0.8117 (pmm) cc_final: 0.7533 (pmm)
REVERT: O 1294 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8883 (mt-10)
REVERT: O 1421 LEU cc_start: 0.9583 (tp) cc_final: 0.9262 (pp)
REVERT: O 1566 CYS cc_start: 0.9509 (m) cc_final: 0.9040 (p)
REVERT: O 1584 PHE cc_start: 0.9140 (m-10) cc_final: 0.8523 (m-80)
REVERT: O 1657 MET cc_start: 0.8497 (mmp) cc_final: 0.8174 (mmp)
REVERT: O 1680 MET cc_start: 0.8390 (mmm) cc_final: 0.8083 (mmm)
REVERT: O 1776 ASP cc_start: 0.8598 (t0) cc_final: 0.8013 (m-30)
REVERT: O 1783 PHE cc_start: 0.9156 (t80) cc_final: 0.8475 (t80)
REVERT: O 1814 MET cc_start: 0.9589 (mtt) cc_final: 0.8844 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0799
  time to fit residues: 9.0692
Evaluate side-chains
  69 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 22 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O1654 GLN
** O1815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.047733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.033562 restraints weight = 41668.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.034770 restraints weight = 26648.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.035630 restraints weight = 19585.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.036170 restraints weight = 15761.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.036611 restraints weight = 13625.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.3388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5904  Z= 0.161
  Angle     :  0.551   9.015   8002  Z= 0.279
  Chirality :  0.041   0.258    887
  Planarity :  0.004   0.037    997
  Dihedral  : 13.027 126.842    925
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.32), residues: 688
  helix:  2.11 (0.29), residues: 330
  sheet:  0.75 (0.42), residues: 132
  loop : -0.05 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG O1175 
 TYR   0.021   0.001   TYR O1195 
 PHE   0.023   0.002   PHE O1669 
 TRP   0.009   0.001   TRP O1166 
 HIS   0.003   0.001   HIS O1574 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.16 ( 5904)
  covalent geometry    : angle       0.55052 /  0.28 ( 8002)
  hydrogen bonds       : bond        0.03018 /  1.97 (  256)
  hydrogen bonds       : angle       4.49480 /  3.28 (  735)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9290 (tpt) cc_final: 0.8814 (tpt)
REVERT: O 1162 LEU cc_start: 0.9782 (mm) cc_final: 0.9422 (pp)
REVERT: O 1166 TRP cc_start: 0.8938 (t-100) cc_final: 0.8655 (t-100)
REVERT: O 1234 ASP cc_start: 0.9404 (m-30) cc_final: 0.9065 (p0)
REVERT: O 1286 MET cc_start: 0.8173 (pmm) cc_final: 0.7509 (pmm)
REVERT: O 1294 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8847 (mp0)
REVERT: O 1421 LEU cc_start: 0.9608 (tp) cc_final: 0.9271 (pp)
REVERT: O 1566 CYS cc_start: 0.9492 (m) cc_final: 0.8952 (p)
REVERT: O 1584 PHE cc_start: 0.9218 (m-10) cc_final: 0.8466 (m-80)
REVERT: O 1657 MET cc_start: 0.8648 (mmp) cc_final: 0.8351 (mmp)
REVERT: O 1760 ARG cc_start: 0.9632 (mtm110) cc_final: 0.9432 (mtm110)
REVERT: O 1776 ASP cc_start: 0.8628 (t0) cc_final: 0.8006 (m-30)
REVERT: O 1783 PHE cc_start: 0.9114 (t80) cc_final: 0.8437 (t80)
REVERT: O 1814 MET cc_start: 0.9484 (mtt) cc_final: 0.8899 (mmm)
REVERT: O 1840 TRP cc_start: 0.9156 (m100) cc_final: 0.8403 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0868
  time to fit residues: 9.2199
Evaluate side-chains
  65 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 52 optimal weight:    8.9990
   chunk 4 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** O1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.046024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.032178 restraints weight = 43547.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.033329 restraints weight = 27678.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.034153 restraints weight = 20373.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.034673 restraints weight = 16403.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.035064 restraints weight = 14235.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   5904  Z= 0.232
  Angle     :  0.623   9.743   8002  Z= 0.313
  Chirality :  0.041   0.255    887
  Planarity :  0.004   0.037    997
  Dihedral  : 13.103 130.808    925
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.32), residues: 688
  helix:  1.95 (0.29), residues: 334
  sheet:  0.82 (0.43), residues: 132
  loop : -0.07 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG O1266 
 TYR   0.026   0.001   TYR O1195 
 PHE   0.010   0.002   PHE O1632 
 TRP   0.008   0.002   TRP O1166 
 HIS   0.005   0.002   HIS O1574 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00472 /  0.23 ( 5904)
  covalent geometry    : angle       0.62337 /  0.31 ( 8002)
  hydrogen bonds       : bond        0.03231 /  2.10 (  256)
  hydrogen bonds       : angle       4.54624 /  3.30 (  735)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9262 (tpt) cc_final: 0.8788 (tpt)
REVERT: O 1114 ASN cc_start: 0.8831 (m-40) cc_final: 0.8545 (m110)
REVERT: O 1157 MET cc_start: 0.8863 (mmm) cc_final: 0.8442 (mmm)
REVERT: O 1162 LEU cc_start: 0.9769 (mm) cc_final: 0.9435 (pp)
REVERT: O 1247 VAL cc_start: 0.9320 (t) cc_final: 0.9022 (p)
REVERT: O 1282 CYS cc_start: 0.9404 (m) cc_final: 0.9037 (m)
REVERT: O 1286 MET cc_start: 0.8416 (pmm) cc_final: 0.7647 (pmm)
REVERT: O 1294 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8863 (mp0)
REVERT: O 1566 CYS cc_start: 0.9469 (m) cc_final: 0.9014 (p)
REVERT: O 1584 PHE cc_start: 0.9353 (m-10) cc_final: 0.8604 (m-80)
REVERT: O 1657 MET cc_start: 0.8743 (mmp) cc_final: 0.8437 (mmp)
REVERT: O 1680 MET cc_start: 0.8361 (mmm) cc_final: 0.8121 (mmm)
REVERT: O 1776 ASP cc_start: 0.8851 (t0) cc_final: 0.8162 (m-30)
REVERT: O 1783 PHE cc_start: 0.9059 (t80) cc_final: 0.8323 (t80)
REVERT: O 1814 MET cc_start: 0.9533 (mtt) cc_final: 0.8906 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0674
  time to fit residues: 6.5311
Evaluate side-chains
  54 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 60 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    0.3980
   chunk 35 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O1265 HIS
O1267 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.047063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.033095 restraints weight = 42305.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.034291 restraints weight = 26526.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.035181 restraints weight = 19361.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.035732 restraints weight = 15443.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.036181 restraints weight = 13318.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.3936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5904  Z= 0.122
  Angle     :  0.545   7.125   8002  Z= 0.275
  Chirality :  0.042   0.252    887
  Planarity :  0.003   0.033    997
  Dihedral  : 13.065 131.895    925
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.33), residues: 688
  helix:  2.07 (0.29), residues: 339
  sheet:  0.84 (0.44), residues: 132
  loop :  0.06 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG O1266 
 TYR   0.011   0.001   TYR O1195 
 PHE   0.006   0.001   PHE O1763 
 TRP   0.041   0.003   TRP O1826 
 HIS   0.002   0.001   HIS O1689 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 ( 5904)
  covalent geometry    : angle       0.54498 /  0.28 ( 8002)
  hydrogen bonds       : bond        0.02781 /  1.81 (  256)
  hydrogen bonds       : angle       4.43330 /  3.18 (  735)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9291 (tpt) cc_final: 0.8834 (tpt)
REVERT: O 1162 LEU cc_start: 0.9767 (mm) cc_final: 0.9379 (pp)
REVERT: O 1219 MET cc_start: 0.8962 (pmm) cc_final: 0.8626 (pmm)
REVERT: O 1247 VAL cc_start: 0.9385 (t) cc_final: 0.9026 (p)
REVERT: O 1282 CYS cc_start: 0.9455 (m) cc_final: 0.9020 (m)
REVERT: O 1286 MET cc_start: 0.8216 (pmm) cc_final: 0.7574 (pmm)
REVERT: O 1294 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8852 (mp0)
REVERT: O 1566 CYS cc_start: 0.9466 (m) cc_final: 0.8940 (p)
REVERT: O 1584 PHE cc_start: 0.9328 (m-10) cc_final: 0.8581 (m-80)
REVERT: O 1657 MET cc_start: 0.8584 (mmp) cc_final: 0.8256 (mmp)
REVERT: O 1680 MET cc_start: 0.8285 (mmm) cc_final: 0.7954 (mmm)
REVERT: O 1760 ARG cc_start: 0.9609 (mtm110) cc_final: 0.9392 (mtm110)
REVERT: O 1776 ASP cc_start: 0.8852 (t0) cc_final: 0.8192 (m-30)
REVERT: O 1783 PHE cc_start: 0.9024 (t80) cc_final: 0.8289 (t80)
REVERT: O 1814 MET cc_start: 0.9485 (mtt) cc_final: 0.8959 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0713
  time to fit residues: 7.1608
Evaluate side-chains
  58 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0870
   chunk 1 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 38 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   overall best weight:    1.1364

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O1114 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.046617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.032737 restraints weight = 41660.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.033910 restraints weight = 26652.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.034745 restraints weight = 19606.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.035287 restraints weight = 15786.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.035723 restraints weight = 13631.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.4062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5904  Z= 0.151
  Angle     :  0.557  11.536   8002  Z= 0.279
  Chirality :  0.042   0.246    887
  Planarity :  0.004   0.035    997
  Dihedral  : 13.081 132.985    925
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.33), residues: 688
  helix:  2.05 (0.29), residues: 338
  sheet:  0.85 (0.44), residues: 132
  loop :  0.05 (0.42), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG O1266 
 TYR   0.012   0.001   TYR O1195 
 PHE   0.009   0.001   PHE O1352 
 TRP   0.048   0.003   TRP O1826 
 HIS   0.002   0.001   HIS O1268 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.15 ( 5904)
  covalent geometry    : angle       0.55734 /  0.28 ( 8002)
  hydrogen bonds       : bond        0.02791 /  1.84 (  256)
  hydrogen bonds       : angle       4.43565 /  3.19 (  735)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9310 (tpt) cc_final: 0.8863 (tpt)
REVERT: O 1162 LEU cc_start: 0.9770 (mm) cc_final: 0.9388 (pp)
REVERT: O 1219 MET cc_start: 0.8958 (pmm) cc_final: 0.8700 (pmm)
REVERT: O 1247 VAL cc_start: 0.9364 (t) cc_final: 0.9007 (p)
REVERT: O 1282 CYS cc_start: 0.9488 (m) cc_final: 0.9098 (m)
REVERT: O 1286 MET cc_start: 0.8167 (pmm) cc_final: 0.7523 (pmm)
REVERT: O 1294 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8856 (mp0)
REVERT: O 1421 LEU cc_start: 0.9636 (tp) cc_final: 0.9348 (pp)
REVERT: O 1566 CYS cc_start: 0.9501 (m) cc_final: 0.8967 (p)
REVERT: O 1584 PHE cc_start: 0.9369 (m-10) cc_final: 0.8597 (m-80)
REVERT: O 1657 MET cc_start: 0.8601 (mmp) cc_final: 0.8214 (mmp)
REVERT: O 1680 MET cc_start: 0.8350 (mmm) cc_final: 0.8025 (mmm)
REVERT: O 1760 ARG cc_start: 0.9613 (mtm110) cc_final: 0.9393 (mtm110)
REVERT: O 1776 ASP cc_start: 0.8886 (t0) cc_final: 0.8239 (m-30)
REVERT: O 1783 PHE cc_start: 0.9043 (t80) cc_final: 0.8264 (t80)
REVERT: O 1814 MET cc_start: 0.9538 (mtt) cc_final: 0.8975 (mpp)
REVERT: O 1840 TRP cc_start: 0.9227 (m100) cc_final: 0.8437 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0721
  time to fit residues: 6.7778
Evaluate side-chains
  57 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 60 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.8782

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.046746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.032860 restraints weight = 41990.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.034045 restraints weight = 26804.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.034891 restraints weight = 19687.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.035438 restraints weight = 15771.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.035877 restraints weight = 13619.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.4146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5904  Z= 0.127
  Angle     :  0.556  13.453   8002  Z= 0.273
  Chirality :  0.042   0.240    887
  Planarity :  0.003   0.034    997
  Dihedral  : 13.060 134.433    925
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.33), residues: 688
  helix:  1.98 (0.29), residues: 338
  sheet:  0.81 (0.44), residues: 132
  loop :  0.04 (0.42), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG O1266 
 TYR   0.010   0.001   TYR O1140 
 PHE   0.007   0.001   PHE O1763 
 TRP   0.031   0.002   TRP O1826 
 HIS   0.002   0.001   HIS O1689 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.13 ( 5904)
  covalent geometry    : angle       0.55638 /  0.27 ( 8002)
  hydrogen bonds       : bond        0.02691 /  1.81 (  256)
  hydrogen bonds       : angle       4.33300 /  3.14 (  735)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9260 (tpt) cc_final: 0.8804 (tpt)
REVERT: O 1116 LEU cc_start: 0.9562 (tt) cc_final: 0.9356 (tt)
REVERT: O 1162 LEU cc_start: 0.9744 (mm) cc_final: 0.9423 (pp)
REVERT: O 1219 MET cc_start: 0.8954 (pmm) cc_final: 0.8672 (pmm)
REVERT: O 1247 VAL cc_start: 0.9337 (t) cc_final: 0.8972 (p)
REVERT: O 1282 CYS cc_start: 0.9425 (m) cc_final: 0.9043 (m)
REVERT: O 1286 MET cc_start: 0.8198 (pmm) cc_final: 0.7570 (pmm)
REVERT: O 1294 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8824 (mp0)
REVERT: O 1421 LEU cc_start: 0.9601 (tp) cc_final: 0.9312 (pp)
REVERT: O 1566 CYS cc_start: 0.9410 (m) cc_final: 0.8929 (p)
REVERT: O 1584 PHE cc_start: 0.9303 (m-10) cc_final: 0.8538 (m-80)
REVERT: O 1657 MET cc_start: 0.8548 (mmp) cc_final: 0.8155 (mmp)
REVERT: O 1680 MET cc_start: 0.8254 (mmm) cc_final: 0.7889 (mmm)
REVERT: O 1760 ARG cc_start: 0.9594 (mtm110) cc_final: 0.9364 (mtm110)
REVERT: O 1776 ASP cc_start: 0.8930 (t0) cc_final: 0.8260 (m-30)
REVERT: O 1783 PHE cc_start: 0.8999 (t80) cc_final: 0.8200 (t80)
REVERT: O 1814 MET cc_start: 0.9491 (mtt) cc_final: 0.8935 (mpp)
REVERT: O 1840 TRP cc_start: 0.9161 (m100) cc_final: 0.8369 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0673
  time to fit residues: 6.3420
Evaluate side-chains
  58 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 46 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0470
   chunk 27 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 68 optimal weight:    0.4980
   overall best weight:    0.6678

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.047023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.033104 restraints weight = 42093.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.034307 restraints weight = 26820.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.035094 restraints weight = 19693.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.035722 restraints weight = 15901.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.036160 restraints weight = 13625.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.4219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5904  Z= 0.112
  Angle     :  0.561  14.404   8002  Z= 0.273
  Chirality :  0.042   0.250    887
  Planarity :  0.003   0.033    997
  Dihedral  : 13.021 134.634    925
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.33), residues: 688
  helix:  2.01 (0.29), residues: 331
  sheet:  0.86 (0.45), residues: 132
  loop :  0.07 (0.41), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG O1266 
 TYR   0.009   0.001   TYR O1140 
 PHE   0.006   0.001   PHE O1763 
 TRP   0.027   0.002   TRP O1826 
 HIS   0.002   0.001   HIS O1689 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.11 ( 5904)
  covalent geometry    : angle       0.56148 /  0.27 ( 8002)
  hydrogen bonds       : bond        0.02515 /  1.70 (  256)
  hydrogen bonds       : angle       4.30887 /  3.13 (  735)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9267 (tpt) cc_final: 0.8819 (tpt)
REVERT: O 1116 LEU cc_start: 0.9577 (tt) cc_final: 0.9372 (tt)
REVERT: O 1162 LEU cc_start: 0.9745 (mm) cc_final: 0.9421 (pp)
REVERT: O 1219 MET cc_start: 0.8934 (pmm) cc_final: 0.8640 (pmm)
REVERT: O 1247 VAL cc_start: 0.9328 (t) cc_final: 0.8974 (p)
REVERT: O 1282 CYS cc_start: 0.9433 (m) cc_final: 0.9053 (m)
REVERT: O 1286 MET cc_start: 0.8112 (pmm) cc_final: 0.7620 (pmm)
REVERT: O 1294 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8823 (mp0)
REVERT: O 1421 LEU cc_start: 0.9594 (tp) cc_final: 0.9302 (pp)
REVERT: O 1566 CYS cc_start: 0.9388 (m) cc_final: 0.8915 (p)
REVERT: O 1584 PHE cc_start: 0.9291 (m-10) cc_final: 0.8513 (m-80)
REVERT: O 1657 MET cc_start: 0.8443 (mmp) cc_final: 0.8020 (mmp)
REVERT: O 1680 MET cc_start: 0.8204 (mmm) cc_final: 0.7831 (mmm)
REVERT: O 1760 ARG cc_start: 0.9586 (mtm110) cc_final: 0.9347 (mtm110)
REVERT: O 1776 ASP cc_start: 0.8944 (t0) cc_final: 0.8294 (m-30)
REVERT: O 1783 PHE cc_start: 0.8973 (t80) cc_final: 0.8166 (t80)
REVERT: O 1814 MET cc_start: 0.9481 (mtt) cc_final: 0.8933 (mpp)
REVERT: O 1840 TRP cc_start: 0.9160 (m100) cc_final: 0.8390 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0654
  time to fit residues: 6.3449
Evaluate side-chains
  59 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 68 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 49 optimal weight:    9.9990
   chunk 61 optimal weight:    0.5980
   chunk 57 optimal weight:    4.9990
   chunk 22 optimal weight:    0.4980
   chunk 60 optimal weight:    0.0970
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.4978

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.047447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.033497 restraints weight = 41616.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.034703 restraints weight = 26551.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.035553 restraints weight = 19534.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.036113 restraints weight = 15730.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.036559 restraints weight = 13568.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.4253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5904  Z= 0.103
  Angle     :  0.544  13.835   8002  Z= 0.265
  Chirality :  0.042   0.235    887
  Planarity :  0.003   0.032    997
  Dihedral  : 12.984 136.376    925
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.33), residues: 688
  helix:  2.05 (0.29), residues: 331
  sheet:  0.89 (0.45), residues: 132
  loop :  0.08 (0.41), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG O1266 
 TYR   0.008   0.001   TYR O1140 
 PHE   0.005   0.001   PHE O1763 
 TRP   0.019   0.002   TRP O1826 
 HIS   0.002   0.001   HIS O1689 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00227 /  0.10 ( 5904)
  covalent geometry    : angle       0.54407 /  0.26 ( 8002)
  hydrogen bonds       : bond        0.02481 /  1.68 (  256)
  hydrogen bonds       : angle       4.25050 /  3.09 (  735)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1045.39 seconds
wall clock time: 18 minutes 49.53 seconds (1129.53 seconds total)