Starting phenix.real_space_refine
on Tue Jan 14 06:31:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rao_19021/01_2025/8rao_19021.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rao_19021/01_2025/8rao_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_19021/01_2025/8rao_19021.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rao_19021/01_2025/8rao_19021.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rao_19021/01_2025/8rao_19021.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rao_19021/01_2025/8rao_19021.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 4.60, per 1000 atoms: 0.80
  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: 1.51
  Conformation dependent library (CDL) restraints added in 769.7 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: 1.86
  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: 2.06

  Time building geometry restraints manager: 1.72 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=" 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
  bond pdb=" N1    C P   4 "
       pdb=" C2    C P   4 "
    ideal  model  delta    sigma   weight residual
    1.397  1.410 -0.013 2.00e-02 2.50e+03 3.96e-01
  ... (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=" 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=" F1  BEF O3003 "
        pdb="BE   BEF O3003 "
        pdb=" F3  BEF O3003 "
      ideal   model   delta    sigma   weight residual
     120.12  110.03   10.09 3.00e+00 1.11e-01 1.13e+01
  angle pdb=" F1  BEF O3003 "
        pdb="BE   BEF O3003 "
        pdb=" F2  BEF O3003 "
      ideal   model   delta    sigma   weight residual
     119.91  112.44    7.47 3.00e+00 1.11e-01 6.20e+00
  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 3.00e+00 1.11e-01 4.88e+00
  angle pdb=" C2'   C P   4 "
        pdb=" C1'   C P   4 "
        pdb=" N1    C P   4 "
      ideal   model   delta    sigma   weight residual
     112.00  114.84   -2.84 1.50e+00 4.44e-01 3.58e+00
  ... (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:             4.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.390
  Find NCS groups from input model:        0.050
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
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= 0.121
  Angle     :  0.462  12.589   8002  Z= 0.220
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.003   0.000   TRP O1688 
 HIS   0.002   0.000   HIS O1574 
 PHE   0.006   0.001   PHE O1860 
 TYR   0.004   0.000   TYR O1195 
 ARG   0.002   0.000   ARG O1820 

*********************** 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  : 0.680 
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: 0.4436 (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: 0.2638
  time to fit residues: 43.0327
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  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 32 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
O1139 ASN
O1555 GLN
O1757 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.050864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.036330 restraints weight = 38897.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.037639 restraints weight = 25047.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.038583 restraints weight = 18367.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2367

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= 0.198
  Angle     :  0.574   8.222   8002  Z= 0.283
  Chirality :  0.043   0.233    887
  Planarity :  0.004   0.046    997
  Dihedral  : 12.830 107.602    925
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 7.06
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.33), residues: 688
  helix:  2.56 (0.30), residues: 338
  sheet:  0.71 (0.44), residues: 131
  loop :  0.00 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP O1166 
 HIS   0.002   0.001   HIS O1574 
 PHE   0.033   0.002   PHE O1763 
 TYR   0.013   0.001   TYR O1117 
 ARG   0.005   0.001   ARG O1820 

*********************** 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
  103 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.775 
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: 0.9386 (tpt) cc_final: 0.8939 (tpt)
REVERT: O 1157 MET cc_start: 0.8831 (mmm) cc_final: 0.8430 (mmm)
REVERT: O 1294 GLU cc_start: 0.9306 (mt-10) cc_final: 0.9086 (mt-10)
REVERT: O 1418 GLU cc_start: 0.9040 (tt0) cc_final: 0.8807 (mt-10)
REVERT: O 1566 CYS cc_start: 0.9537 (m) cc_final: 0.9191 (p)
REVERT: O 1584 PHE cc_start: 0.8877 (m-80) cc_final: 0.8541 (m-80)
REVERT: O 1613 MET cc_start: 0.9579 (mtm) cc_final: 0.9075 (mtp)
REVERT: O 1776 ASP cc_start: 0.8650 (t0) cc_final: 0.7960 (m-30)
REVERT: O 1783 PHE cc_start: 0.9071 (t80) cc_final: 0.8303 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.2291
  time to fit residues: 29.8944
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  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 61 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 46 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 38 optimal weight:    0.3980
   chunk 37 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
O1241 HIS
O1309 GLN
O1312 GLN
** O1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.049948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.035478 restraints weight = 39595.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.036743 restraints weight = 25525.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.037656 restraints weight = 18776.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5904  Z= 0.180
  Angle     :  0.555   8.915   8002  Z= 0.269
  Chirality :  0.041   0.173    887
  Planarity :  0.004   0.039    997
  Dihedral  : 12.718 105.618    925
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 7.32
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.33), residues: 688
  helix:  2.34 (0.30), residues: 337
  sheet:  0.74 (0.43), residues: 133
  loop :  0.23 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP O1840 
 HIS   0.002   0.001   HIS O1830 
 PHE   0.023   0.001   PHE O1763 
 TYR   0.019   0.001   TYR O1140 
 ARG   0.004   0.000   ARG O1641 

*********************** 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
  89 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.700 
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: O 1105 MET cc_start: 0.9352 (tpt) cc_final: 0.8918 (tpt)
REVERT: O 1157 MET cc_start: 0.8897 (mmm) cc_final: 0.8577 (mmm)
REVERT: O 1162 LEU cc_start: 0.9782 (mm) cc_final: 0.9484 (pp)
REVERT: O 1166 TRP cc_start: 0.8966 (t-100) cc_final: 0.8682 (t-100)
REVERT: O 1192 SER cc_start: 0.8760 (m) cc_final: 0.8251 (p)
REVERT: O 1294 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9074 (mt-10)
REVERT: O 1421 LEU cc_start: 0.9540 (tp) cc_final: 0.9221 (pp)
REVERT: O 1566 CYS cc_start: 0.9512 (m) cc_final: 0.8957 (p)
REVERT: O 1584 PHE cc_start: 0.9106 (m-80) cc_final: 0.8521 (m-80)
REVERT: O 1613 MET cc_start: 0.9584 (mtm) cc_final: 0.8229 (mtm)
REVERT: O 1657 MET cc_start: 0.8527 (mmp) cc_final: 0.8296 (mmp)
REVERT: O 1680 MET cc_start: 0.8376 (mmm) cc_final: 0.8082 (mmm)
REVERT: O 1776 ASP cc_start: 0.8583 (t0) cc_final: 0.8061 (m-30)
REVERT: O 1783 PHE cc_start: 0.9052 (t80) cc_final: 0.8275 (t80)
REVERT: O 1814 MET cc_start: 0.9560 (mtt) cc_final: 0.8949 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.2351
  time to fit residues: 26.5700
Evaluate side-chains
  71 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 52 optimal weight:    7.9990
   chunk 63 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 46 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
O1241 HIS
** O1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O1831 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.047302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.033147 restraints weight = 42290.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.034352 restraints weight = 26837.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.035191 restraints weight = 19667.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.3399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5904  Z= 0.248
  Angle     :  0.581   8.155   8002  Z= 0.286
  Chirality :  0.040   0.185    887
  Planarity :  0.004   0.045    997
  Dihedral  : 12.755 107.166    925
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.33), residues: 688
  helix:  2.26 (0.29), residues: 333
  sheet:  0.80 (0.43), residues: 133
  loop :  0.05 (0.42), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP O1840 
 HIS   0.004   0.001   HIS O1241 
 PHE   0.015   0.001   PHE O1777 
 TYR   0.014   0.001   TYR O1198 
 ARG   0.006   0.001   ARG O1175 

*********************** 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
  81 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.612 
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: 0.9333 (tpt) cc_final: 0.8872 (tpt)
REVERT: O 1157 MET cc_start: 0.8938 (mmm) cc_final: 0.8530 (mmm)
REVERT: O 1162 LEU cc_start: 0.9792 (mm) cc_final: 0.9415 (pp)
REVERT: O 1192 SER cc_start: 0.8802 (m) cc_final: 0.8273 (p)
REVERT: O 1234 ASP cc_start: 0.9416 (m-30) cc_final: 0.9068 (p0)
REVERT: O 1247 VAL cc_start: 0.9376 (t) cc_final: 0.8958 (p)
REVERT: O 1286 MET cc_start: 0.8895 (ptp) cc_final: 0.8633 (ptp)
REVERT: O 1421 LEU cc_start: 0.9644 (tp) cc_final: 0.9324 (pp)
REVERT: O 1566 CYS cc_start: 0.9508 (m) cc_final: 0.8948 (p)
REVERT: O 1584 PHE cc_start: 0.9388 (m-80) cc_final: 0.8752 (m-80)
REVERT: O 1613 MET cc_start: 0.9615 (mtm) cc_final: 0.9305 (mtp)
REVERT: O 1638 LEU cc_start: 0.9756 (tp) cc_final: 0.9432 (mt)
REVERT: O 1776 ASP cc_start: 0.8671 (t0) cc_final: 0.8092 (m-30)
REVERT: O 1783 PHE cc_start: 0.9168 (t80) cc_final: 0.8485 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2207
  time to fit residues: 22.7451
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  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 68 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 67 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** O1757 GLN ** 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 = 0.3273 r_free = 0.3273 target = 0.047936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.033640 restraints weight = 41159.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.034884 restraints weight = 26404.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.035702 restraints weight = 19407.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.3567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5904  Z= 0.172
  Angle     :  0.544   8.683   8002  Z= 0.263
  Chirality :  0.040   0.184    887
  Planarity :  0.003   0.044    997
  Dihedral  : 12.715 110.028    925
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.33), residues: 688
  helix:  2.28 (0.29), residues: 333
  sheet:  0.92 (0.44), residues: 131
  loop :  0.10 (0.42), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP O1840 
 HIS   0.003   0.001   HIS O1658 
 PHE   0.007   0.001   PHE O1733 
 TYR   0.010   0.001   TYR O1140 
 ARG   0.012   0.000   ARG O1266 

*********************** 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
  80 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.727 
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: O 1105 MET cc_start: 0.9341 (tpt) cc_final: 0.8882 (tpt)
REVERT: O 1157 MET cc_start: 0.8926 (mmm) cc_final: 0.8650 (mmm)
REVERT: O 1162 LEU cc_start: 0.9780 (mm) cc_final: 0.9412 (pp)
REVERT: O 1234 ASP cc_start: 0.9407 (m-30) cc_final: 0.9114 (p0)
REVERT: O 1247 VAL cc_start: 0.9328 (t) cc_final: 0.8992 (p)
REVERT: O 1286 MET cc_start: 0.8696 (ptp) cc_final: 0.7996 (pmm)
REVERT: O 1288 MET cc_start: 0.9301 (mmp) cc_final: 0.9092 (mmm)
REVERT: O 1566 CYS cc_start: 0.9477 (m) cc_final: 0.8915 (p)
REVERT: O 1584 PHE cc_start: 0.9378 (m-80) cc_final: 0.8762 (m-80)
REVERT: O 1613 MET cc_start: 0.9617 (mtm) cc_final: 0.9038 (mtp)
REVERT: O 1638 LEU cc_start: 0.9742 (tp) cc_final: 0.9396 (mt)
REVERT: O 1642 MET cc_start: 0.8477 (mmm) cc_final: 0.8134 (mmm)
REVERT: O 1657 MET cc_start: 0.8671 (mmp) cc_final: 0.8465 (mmp)
REVERT: O 1776 ASP cc_start: 0.8784 (t0) cc_final: 0.8227 (m-30)
REVERT: O 1783 PHE cc_start: 0.9149 (t80) cc_final: 0.8485 (t80)
REVERT: O 1814 MET cc_start: 0.9628 (mtt) cc_final: 0.8903 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.1950
  time to fit residues: 20.5910
Evaluate side-chains
  64 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 12 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 61 optimal weight:    9.9990
   chunk 0 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    0.9588

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

Flipped N/Q/H residues before XYZ refinement:
** O1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1757 GLN ** 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 = 0.3266 r_free = 0.3266 target = 0.047548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.033596 restraints weight = 41383.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.034788 restraints weight = 26560.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.035604 restraints weight = 19533.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5904  Z= 0.182
  Angle     :  0.546   9.997   8002  Z= 0.264
  Chirality :  0.040   0.185    887
  Planarity :  0.004   0.042    997
  Dihedral  : 12.742 113.132    925
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.33), residues: 688
  helix:  2.18 (0.29), residues: 333
  sheet:  0.92 (0.44), residues: 131
  loop :  0.06 (0.42), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP O1826 
 HIS   0.002   0.001   HIS O1689 
 PHE   0.010   0.001   PHE O1669 
 TYR   0.009   0.001   TYR O1140 
 ARG   0.006   0.000   ARG O1266 

*********************** 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
  76 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.699 
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: 0.9339 (tpt) cc_final: 0.8880 (tpt)
REVERT: O 1162 LEU cc_start: 0.9775 (mm) cc_final: 0.9352 (pp)
REVERT: O 1247 VAL cc_start: 0.9346 (t) cc_final: 0.8952 (p)
REVERT: O 1282 CYS cc_start: 0.9488 (m) cc_final: 0.9049 (m)
REVERT: O 1421 LEU cc_start: 0.9626 (tp) cc_final: 0.9338 (pp)
REVERT: O 1566 CYS cc_start: 0.9472 (m) cc_final: 0.8930 (p)
REVERT: O 1584 PHE cc_start: 0.9400 (m-80) cc_final: 0.8780 (m-80)
REVERT: O 1613 MET cc_start: 0.9627 (mtm) cc_final: 0.9277 (mtp)
REVERT: O 1680 MET cc_start: 0.8183 (mmm) cc_final: 0.7877 (mmm)
REVERT: O 1776 ASP cc_start: 0.8802 (t0) cc_final: 0.8267 (m-30)
REVERT: O 1783 PHE cc_start: 0.9107 (t80) cc_final: 0.8386 (t80)
REVERT: O 1814 MET cc_start: 0.9521 (mtt) cc_final: 0.8949 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1893
  time to fit residues: 19.4029
Evaluate side-chains
  62 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 49 optimal weight:    9.9990
   chunk 68 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0870
   chunk 51 optimal weight:    0.9980
   chunk 35 optimal weight:    7.9990
   overall best weight:    1.0164

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

Flipped N/Q/H residues before XYZ refinement:
** O1636 GLN ** 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 = 0.3258 r_free = 0.3258 target = 0.047159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.033145 restraints weight = 41478.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.034333 restraints weight = 26777.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.035124 restraints weight = 19870.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.4038

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= 0.191
  Angle     :  0.546   7.482   8002  Z= 0.265
  Chirality :  0.040   0.186    887
  Planarity :  0.004   0.045    997
  Dihedral  : 12.800 116.088    925
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.33), residues: 688
  helix:  2.18 (0.29), residues: 331
  sheet:  0.89 (0.44), residues: 131
  loop :  0.06 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP O1826 
 HIS   0.003   0.001   HIS O1268 
 PHE   0.008   0.001   PHE O1669 
 TYR   0.009   0.001   TYR O1198 
 ARG   0.005   0.000   ARG O1266 

*********************** 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  : 0.614 
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: 0.9306 (tpt) cc_final: 0.8850 (tpt)
REVERT: O 1157 MET cc_start: 0.8813 (mmm) cc_final: 0.8508 (mmm)
REVERT: O 1162 LEU cc_start: 0.9765 (mm) cc_final: 0.9327 (pp)
REVERT: O 1247 VAL cc_start: 0.9335 (t) cc_final: 0.8970 (p)
REVERT: O 1282 CYS cc_start: 0.9449 (m) cc_final: 0.9054 (m)
REVERT: O 1286 MET cc_start: 0.8611 (ptp) cc_final: 0.7859 (pmm)
REVERT: O 1288 MET cc_start: 0.9334 (mmp) cc_final: 0.9114 (mmm)
REVERT: O 1566 CYS cc_start: 0.9406 (m) cc_final: 0.8872 (p)
REVERT: O 1584 PHE cc_start: 0.9372 (m-80) cc_final: 0.8816 (m-80)
REVERT: O 1613 MET cc_start: 0.9575 (mtm) cc_final: 0.9009 (mtp)
REVERT: O 1638 LEU cc_start: 0.9673 (tp) cc_final: 0.9401 (mt)
REVERT: O 1642 MET cc_start: 0.8472 (mmm) cc_final: 0.8186 (mmm)
REVERT: O 1657 MET cc_start: 0.8744 (mmp) cc_final: 0.8494 (mmp)
REVERT: O 1680 MET cc_start: 0.8207 (mmm) cc_final: 0.7785 (mmm)
REVERT: O 1776 ASP cc_start: 0.8866 (t0) cc_final: 0.8321 (m-30)
REVERT: O 1783 PHE cc_start: 0.9030 (t80) cc_final: 0.8270 (t80)
REVERT: O 1814 MET cc_start: 0.9519 (mtt) cc_final: 0.8974 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1959
  time to fit residues: 19.6448
Evaluate side-chains
  61 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 9 optimal weight:    0.4980
   chunk 47 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** O1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O1645 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.047193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.033279 restraints weight = 41034.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.034466 restraints weight = 26565.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.035316 restraints weight = 19637.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.4130

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= 0.162
  Angle     :  0.551  12.058   8002  Z= 0.266
  Chirality :  0.040   0.184    887
  Planarity :  0.003   0.040    997
  Dihedral  : 12.806 117.804    925
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.33), residues: 688
  helix:  2.10 (0.29), residues: 338
  sheet:  0.83 (0.44), residues: 131
  loop :  0.11 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP O1826 
 HIS   0.002   0.001   HIS O1689 
 PHE   0.009   0.001   PHE O1763 
 TYR   0.008   0.001   TYR O1198 
 ARG   0.005   0.000   ARG O1266 

*********************** 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
  73 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.699 
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: O 1105 MET cc_start: 0.9305 (tpt) cc_final: 0.8854 (tpt)
REVERT: O 1157 MET cc_start: 0.8769 (mmm) cc_final: 0.8538 (mmm)
REVERT: O 1162 LEU cc_start: 0.9762 (mm) cc_final: 0.9374 (pp)
REVERT: O 1247 VAL cc_start: 0.9262 (t) cc_final: 0.8867 (p)
REVERT: O 1282 CYS cc_start: 0.9455 (m) cc_final: 0.9058 (m)
REVERT: O 1286 MET cc_start: 0.8797 (ptp) cc_final: 0.7842 (pmm)
REVERT: O 1288 MET cc_start: 0.9267 (mmp) cc_final: 0.9058 (mmm)
REVERT: O 1566 CYS cc_start: 0.9382 (m) cc_final: 0.8856 (p)
REVERT: O 1584 PHE cc_start: 0.9355 (m-80) cc_final: 0.8798 (m-80)
REVERT: O 1613 MET cc_start: 0.9548 (mtm) cc_final: 0.8984 (mtp)
REVERT: O 1638 LEU cc_start: 0.9675 (tp) cc_final: 0.9405 (mt)
REVERT: O 1642 MET cc_start: 0.8408 (mmm) cc_final: 0.8093 (mmm)
REVERT: O 1680 MET cc_start: 0.8219 (mmm) cc_final: 0.7746 (mmm)
REVERT: O 1776 ASP cc_start: 0.8909 (t0) cc_final: 0.8329 (m-30)
REVERT: O 1783 PHE cc_start: 0.8995 (t80) cc_final: 0.8243 (t80)
REVERT: O 1814 MET cc_start: 0.9583 (mtp) cc_final: 0.9177 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.1891
  time to fit residues: 18.3529
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  : 0.619 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 52 optimal weight:    0.4980
   chunk 45 optimal weight:    1.9990
   chunk 55 optimal weight:    7.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** O1636 GLN ** 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 = 0.3259 r_free = 0.3259 target = 0.047358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.033209 restraints weight = 41780.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.034407 restraints weight = 26645.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.035290 restraints weight = 19580.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.4281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5904  Z= 0.165
  Angle     :  0.555  13.577   8002  Z= 0.267
  Chirality :  0.040   0.188    887
  Planarity :  0.003   0.040    997
  Dihedral  : 12.772 120.577    925
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.33), residues: 688
  helix:  2.06 (0.29), residues: 338
  sheet:  0.74 (0.45), residues: 131
  loop :  0.15 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP O1826 
 HIS   0.002   0.001   HIS O1689 
 PHE   0.007   0.001   PHE O1669 
 TYR   0.009   0.001   TYR O1198 
 ARG   0.005   0.000   ARG O1266 

*********************** 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
  71 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.528 
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: 0.9298 (tpt) cc_final: 0.8856 (tpt)
REVERT: O 1162 LEU cc_start: 0.9760 (mm) cc_final: 0.9373 (pp)
REVERT: O 1247 VAL cc_start: 0.9240 (t) cc_final: 0.8851 (p)
REVERT: O 1282 CYS cc_start: 0.9447 (m) cc_final: 0.9018 (m)
REVERT: O 1566 CYS cc_start: 0.9400 (m) cc_final: 0.8867 (p)
REVERT: O 1584 PHE cc_start: 0.9361 (m-80) cc_final: 0.8817 (m-80)
REVERT: O 1613 MET cc_start: 0.9523 (mtm) cc_final: 0.8943 (mtp)
REVERT: O 1638 LEU cc_start: 0.9671 (tp) cc_final: 0.9421 (mt)
REVERT: O 1642 MET cc_start: 0.8459 (mmm) cc_final: 0.8131 (mmm)
REVERT: O 1680 MET cc_start: 0.8268 (mmm) cc_final: 0.7772 (mmm)
REVERT: O 1776 ASP cc_start: 0.8958 (t0) cc_final: 0.8346 (m-30)
REVERT: O 1783 PHE cc_start: 0.8984 (t80) cc_final: 0.8217 (t80)
REVERT: O 1814 MET cc_start: 0.9585 (mtp) cc_final: 0.9157 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1937
  time to fit residues: 18.1575
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  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 2 optimal weight:    0.1980
   chunk 59 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
O1636 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.047635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.033271 restraints weight = 41411.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.034472 restraints weight = 26821.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.035326 restraints weight = 19860.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.4365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5904  Z= 0.150
  Angle     :  0.575  13.777   8002  Z= 0.273
  Chirality :  0.040   0.184    887
  Planarity :  0.003   0.040    997
  Dihedral  : 12.720 119.364    925
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.33), residues: 688
  helix:  2.11 (0.29), residues: 337
  sheet:  0.68 (0.45), residues: 131
  loop :  0.20 (0.42), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP O1826 
 HIS   0.002   0.001   HIS O1265 
 PHE   0.006   0.001   PHE O1669 
 TYR   0.013   0.001   TYR O1195 
 ARG   0.004   0.000   ARG O1266 

********************** 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
  74 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.745 
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: 0.9304 (tpt) cc_final: 0.8868 (tpt)
REVERT: O 1157 MET cc_start: 0.8650 (mmp) cc_final: 0.8334 (mmm)
REVERT: O 1162 LEU cc_start: 0.9751 (mm) cc_final: 0.9357 (pp)
REVERT: O 1247 VAL cc_start: 0.9211 (t) cc_final: 0.8808 (p)
REVERT: O 1286 MET cc_start: 0.8988 (ptp) cc_final: 0.8396 (ptp)
REVERT: O 1566 CYS cc_start: 0.9349 (m) cc_final: 0.8835 (p)
REVERT: O 1584 PHE cc_start: 0.9381 (m-80) cc_final: 0.8817 (m-80)
REVERT: O 1613 MET cc_start: 0.9541 (mtm) cc_final: 0.8020 (mtm)
REVERT: O 1680 MET cc_start: 0.8258 (mmm) cc_final: 0.7772 (mmm)
REVERT: O 1776 ASP cc_start: 0.8987 (t0) cc_final: 0.8370 (m-30)
REVERT: O 1783 PHE cc_start: 0.8971 (t80) cc_final: 0.8243 (t80)
REVERT: O 1814 MET cc_start: 0.9578 (mtp) cc_final: 0.9111 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1822
  time to fit residues: 18.0639
Evaluate side-chains
  56 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 67 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3261 r_free = 0.3261 target = 0.047385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.033232 restraints weight = 42163.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.034413 restraints weight = 27304.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.035209 restraints weight = 20218.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.4488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5904  Z= 0.163
  Angle     :  0.588  13.419   8002  Z= 0.278
  Chirality :  0.041   0.183    887
  Planarity :  0.003   0.040    997
  Dihedral  : 12.747 118.969    925
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.33), residues: 688
  helix:  2.05 (0.29), residues: 338
  sheet:  0.67 (0.45), residues: 131
  loop :  0.16 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP O1826 
 HIS   0.006   0.001   HIS O1265 
 PHE   0.008   0.001   PHE O1374 
 TYR   0.009   0.001   TYR O1198 
 ARG   0.004   0.000   ARG O1641 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2021.15 seconds
wall clock time: 37 minutes 25.03 seconds (2245.03 seconds total)