Starting phenix.real_space_refine
on Tue Feb  3 15:54:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n5o_48941/02_2026/9n5o_48941.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n5o_48941/02_2026/9n5o_48941.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n5o_48941/02_2026/9n5o_48941.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n5o_48941/02_2026/9n5o_48941.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n5o_48941/02_2026/9n5o_48941.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n5o_48941/02_2026/9n5o_48941.cif"
  }
  resolution = 4.32
  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=   0.001 sd=   0.009
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: 4
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     C    2794      2.51       5
     N     734      2.21       5
     O     864      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4415
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 2696
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2696
          Classifications: {'peptide': 336}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 318}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 909
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "L"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 810
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99}
  Time building chain proxies: 1.15, per 1000 atoms: 0.26
  Number of scatterers: 4415
  At special positions: 0
  Unit cell: (92.07, 93, 91.14, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      23     16.00
     O     864      8.00
     N     734      7.00
     C    2794      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS B1698 " - pdb=" SG  CYS B1726 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1740 " - pdb=" SG  CYS B1881 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1914 " - pdb=" SG  CYS B1938 " distance=2.09
    Simple disulfide: pdb=" SG  CYS B1952 " - pdb=" SG  CYS B2017 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1963 " - pdb=" SG  CYS B2015 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=1.99
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=1.98

  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: 0.34
  Conformation dependent library (CDL) restraints added in 167.9 milliseconds
  

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1056

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 13 sheets defined
      11.4% alpha, 43.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'B' and resid 1708 through 1713
    Processing helix  chain 'B' and resid 1743 through 1754
      removed outlier: 3.917A  pdb=" N   VAL B1752 " --> pdb=" O   GLU B1748 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1759 through 1770
    Processing helix  chain 'B' and resid 1804 through 1811
    Processing helix  chain 'B' and resid 1838 through 1842
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.563A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 60 through 65
      removed outlier: 4.548A  pdb=" N   GLY H  65 " --> pdb=" O   GLN H  61 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.921A  pdb=" N   LEU L  83 " --> pdb=" O   ALA L  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 1684 through 1687
      removed outlier: 6.385A  pdb=" N   LYS B1684 " --> pdb=" O   HIS B1725 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   TYR B1727 " --> pdb=" O   LYS B1684 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   MET B1686 " --> pdb=" O   TYR B1727 " (cutoff:3.500A)
      removed outlier: 8.554A  pdb=" N   LEU B1729 " --> pdb=" O   MET B1686 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   ILE B1724 " --> pdb=" O   ILE B1899 " (cutoff:3.500A)
      removed outlier: 8.090A  pdb=" N   HIS B1901 " --> pdb=" O   ILE B1724 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   CYS B1726 " --> pdb=" O   HIS B1901 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   ASP B1903 " --> pdb=" O   CYS B1726 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   ALA B1728 " --> pdb=" O   ASP B1903 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 1684 through 1687
      removed outlier: 6.385A  pdb=" N   LYS B1684 " --> pdb=" O   HIS B1725 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   TYR B1727 " --> pdb=" O   LYS B1684 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   MET B1686 " --> pdb=" O   TYR B1727 " (cutoff:3.500A)
      removed outlier: 8.554A  pdb=" N   LEU B1729 " --> pdb=" O   MET B1686 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   ILE B1724 " --> pdb=" O   ILE B1899 " (cutoff:3.500A)
      removed outlier: 8.090A  pdb=" N   HIS B1901 " --> pdb=" O   ILE B1724 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   CYS B1726 " --> pdb=" O   HIS B1901 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   ASP B1903 " --> pdb=" O   CYS B1726 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   ALA B1728 " --> pdb=" O   ASP B1903 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ILE B1826 " --> pdb=" O   LYS B1878 " (cutoff:3.500A)
      removed outlier: 8.678A  pdb=" N   GLU B1880 " --> pdb=" O   LYS B1824 " (cutoff:3.500A)
      removed outlier: 11.983A  pdb=" N   LYS B1824 " --> pdb=" O   GLU B1880 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 1689 through 1691
      removed outlier: 6.280A  pdb=" N   HIS B1696 " --> pdb=" O   TYR B1737 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   LYS B1739 " --> pdb=" O   HIS B1696 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   CYS B1698 " --> pdb=" O   LYS B1739 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 1689 through 1691
      removed outlier: 6.280A  pdb=" N   HIS B1696 " --> pdb=" O   TYR B1737 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   LYS B1739 " --> pdb=" O   HIS B1696 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   CYS B1698 " --> pdb=" O   LYS B1739 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1937 through 1942
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1947 through 1951
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1966 through 1969
    Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.763A  pdb=" N   MET H  34 " --> pdb=" O   ALA H  50 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   ALA H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   TRP H  36 " --> pdb=" O   PHE H  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.897A  pdb=" N   TYR H 102 " --> pdb=" O   ARG H  94 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 5
    Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.187A  pdb=" N   MET L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA L  84 " --> pdb=" O   LEU L 104 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   VAL L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   TYR L  49 " --> pdb=" O   VAL L  33 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.187A  pdb=" N   MET L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA L  84 " --> pdb=" O   LEU L 104 " (cutoff:3.500A)

    174 hydrogen bonds defined for protein.
    420 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.53

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1389
        1.34 -     1.47: 1111
        1.47 -     1.60: 1977
        1.60 -     1.73: 0
        1.73 -     1.85: 32
  Bond restraints: 4509
  Sorted by residual:
  bond pdb=" CG  LEU L  83 "
       pdb=" CD2 LEU L  83 "
    ideal  model  delta    sigma   weight residual
    1.521  1.407  0.114 3.30e-02 9.18e+02 1.19e+01
  bond pdb=" CB  ILE B1841 "
       pdb=" CG2 ILE B1841 "
    ideal  model  delta    sigma   weight residual
    1.521  1.443  0.078 3.30e-02 9.18e+02 5.54e+00
  bond pdb=" CG1 ILE B1942 "
       pdb=" CD1 ILE B1942 "
    ideal  model  delta    sigma   weight residual
    1.513  1.431  0.082 3.90e-02 6.57e+02 4.37e+00
  bond pdb=" CG  GLU B1966 "
       pdb=" CD  GLU B1966 "
    ideal  model  delta    sigma   weight residual
    1.516  1.567 -0.051 2.50e-02 1.60e+03 4.18e+00
  bond pdb=" CB  ASP B2006 "
       pdb=" CG  ASP B2006 "
    ideal  model  delta    sigma   weight residual
    1.516  1.567 -0.051 2.50e-02 1.60e+03 4.18e+00
  ... (remaining 4504 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 5893
        2.75 -     5.51: 186
        5.51 -     8.26: 14
        8.26 -    11.02: 1
       11.02 -    13.77: 1
  Bond angle restraints: 6095
  Sorted by residual:
  angle pdb=" N   GLY B1913 "
        pdb=" CA  GLY B1913 "
        pdb=" C   GLY B1913 "
      ideal   model   delta    sigma   weight residual
     113.18  124.13  -10.95 2.37e+00 1.78e-01 2.13e+01
  angle pdb=" CA  TYR B2007 "
        pdb=" CB  TYR B2007 "
        pdb=" CG  TYR B2007 "
      ideal   model   delta    sigma   weight residual
     113.90  122.03   -8.13 1.80e+00 3.09e-01 2.04e+01
  angle pdb=" N   SER B1894 "
        pdb=" CA  SER B1894 "
        pdb=" C   SER B1894 "
      ideal   model   delta    sigma   weight residual
     108.46  114.93   -6.47 1.51e+00 4.39e-01 1.84e+01
  angle pdb=" C   LYS B1973 "
        pdb=" N   THR B1974 "
        pdb=" CA  THR B1974 "
      ideal   model   delta    sigma   weight residual
     121.85  114.44    7.41 1.77e+00 3.19e-01 1.75e+01
  angle pdb=" C   PHE B1822 "
        pdb=" N   GLU B1823 "
        pdb=" CA  GLU B1823 "
      ideal   model   delta    sigma   weight residual
     120.58  113.80    6.78 1.71e+00 3.42e-01 1.57e+01
  ... (remaining 6090 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.35: 2624
       16.35 -    32.70: 88
       32.70 -    49.04: 21
       49.04 -    65.39: 10
       65.39 -    81.74: 7
  Dihedral angle restraints: 2750
    sinusoidal: 1110
      harmonic: 1640
  Sorted by residual:
  dihedral pdb=" CA  SER B1848 "
           pdb=" C   SER B1848 "
           pdb=" N   PRO B1849 "
           pdb=" CA  PRO B1849 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.68   23.32     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  SER H  95 "
           pdb=" C   SER H  95 "
           pdb=" N   LEU H  96 "
           pdb=" CA  LEU H  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.46   22.54     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" CA  TYR H  59 "
           pdb=" C   TYR H  59 "
           pdb=" N   THR H  60 "
           pdb=" CA  THR H  60 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.86   21.14     0      5.00e+00 4.00e-02 1.79e+01
  ... (remaining 2747 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 384
       0.038 -    0.075: 179
       0.075 -    0.113: 68
       0.113 -    0.151: 28
       0.151 -    0.188: 11
  Chirality restraints: 670
  Sorted by residual:
  chirality pdb=" CB  ILE B1706 "
            pdb=" CA  ILE B1706 "
            pdb=" CG1 ILE B1706 "
            pdb=" CG2 ILE B1706 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.19 2.00e-01 2.50e+01 8.86e-01
  chirality pdb=" CA  ILE B1967 "
            pdb=" N   ILE B1967 "
            pdb=" C   ILE B1967 "
            pdb=" CB  ILE B1967 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.78e-01
  chirality pdb=" CB  ILE B1841 "
            pdb=" CA  ILE B1841 "
            pdb=" CG1 ILE B1841 "
            pdb=" CG2 ILE B1841 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.73e-01
  ... (remaining 667 not shown)

  Planarity restraints: 783
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B1813 "    0.017 2.00e-02 2.50e+03   3.47e-02 1.20e+01
        pdb=" C   ASN B1813 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   ASN B1813 "    0.022 2.00e-02 2.50e+03
        pdb=" N   ILE B1814 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA L  51 "   -0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" C   ALA L  51 "    0.055 2.00e-02 2.50e+03
        pdb=" O   ALA L  51 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   SER L  52 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B2007 "    0.033 2.00e-02 2.50e+03   2.14e-02 9.18e+00
        pdb=" CG  TYR B2007 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 TYR B2007 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR B2007 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR B2007 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B2007 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR B2007 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B2007 "    0.006 2.00e-02 2.50e+03
  ... (remaining 780 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1283
        2.83 -     3.34: 4012
        3.34 -     3.86: 7516
        3.86 -     4.38: 8967
        4.38 -     4.90: 14573
  Nonbonded interactions: 36351
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS L  24 "
            pdb=" OD1 ASP L  70 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" N   LEU B1733 "
            pdb=" O   VAL B1867 "
     model   vdw
     2.359 3.120
  nonbonded pdb=" OE1 GLU B1715 "
            pdb=" NZ  LYS B1887 "
     model   vdw
     2.396 3.120
  nonbonded pdb=" O   ASP B1959 "
            pdb=" OG  SER B2016 "
     model   vdw
     2.401 3.040
  nonbonded pdb=" NZ  LYS B1739 "
            pdb=" O   LYS B1771 "
     model   vdw
     2.408 3.120
  ... (remaining 36346 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:             2.550
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.390
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5167
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      :  0.008   0.114   4516  Z= 0.366
  Angle     :  1.116  13.773   6109  Z= 0.648
  Chirality :  0.055   0.188    670
  Planarity :  0.007   0.065    783
  Dihedral  : 10.746  81.738   1673
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  1.00 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.35), residues: 551
  helix: -1.02 (0.70), residues: 41
  sheet:  0.20 (0.41), residues: 155
  loop : -0.84 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B1695 
 TYR   0.049   0.004   TYR B2007 
 PHE   0.044   0.005   PHE B1821 
 TRP   0.017   0.003   TRP H  47 
 HIS   0.010   0.003   HIS B2021 

Details of bonding type rmsd
  covalent geometry    : bond        0.00773 ( 4509)
  covalent geometry    : angle       1.11383 ( 6095)
  SS BOND              : bond        0.03331 (    7)
  SS BOND              : angle       1.86928 (   14)
  hydrogen bonds       : bond        0.13583 (  144)
  hydrogen bonds       : angle       8.27252 (  420)

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 119
  time to evaluate  : 0.175 
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: B 1729 LEU cc_start: 0.9278 (tp) cc_final: 0.8855 (tp)
REVERT: B 1778 THR cc_start: 0.9579 (p) cc_final: 0.9252 (t)
REVERT: B 1850 MET cc_start: 0.7967 (ttt) cc_final: 0.7738 (tpp)
REVERT: B 1893 ILE cc_start: 0.9497 (pt) cc_final: 0.9265 (mp)
REVERT: H   31 ASN cc_start: 0.9455 (m-40) cc_final: 0.9232 (t0)
REVERT: H   34 MET cc_start: 0.4085 (tpp) cc_final: 0.3442 (mmm)
REVERT: H   72 ASP cc_start: 0.9428 (t0) cc_final: 0.8962 (p0)
REVERT: L   53 TYR cc_start: 0.9390 (m-80) cc_final: 0.9048 (m-10)
REVERT: L   55 TYR cc_start: 0.8165 (t80) cc_final: 0.7860 (t80)
REVERT: L   87 TYR cc_start: 0.8503 (m-80) cc_final: 0.7875 (m-10)
  outliers start: 2
  outliers final: 1
  residues processed: 120
  average time/residue: 0.0848
  time to fit residues: 12.2027
Evaluate side-chains
  55 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:   20.0000
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 50 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
B1774 HIS
B1891 GLN
B1991 HIS
H   5 GLN
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.093850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.083592 restraints weight = 46524.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.085533 restraints weight = 44007.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.086246 restraints weight = 31203.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.086842 restraints weight = 26617.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.087221 restraints weight = 23672.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.4294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5390
moved from start:          0.3953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   4516  Z= 0.181
  Angle     :  0.756  10.563   6109  Z= 0.406
  Chirality :  0.046   0.166    670
  Planarity :  0.005   0.051    783
  Dihedral  :  6.314  24.325    595
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.36), residues: 551
  helix:  0.26 (0.89), residues: 36
  sheet: -0.03 (0.38), residues: 189
  loop : -0.78 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG H  58 
 TYR   0.023   0.002   TYR B2007 
 PHE   0.037   0.002   PHE B1978 
 TRP   0.022   0.003   TRP H  33 
 HIS   0.003   0.001   HIS B1991 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 4509)
  covalent geometry    : angle       0.75580 ( 6095)
  SS BOND              : bond        0.00801 (    7)
  SS BOND              : angle       0.99353 (   14)
  hydrogen bonds       : bond        0.04205 (  144)
  hydrogen bonds       : angle       6.66808 (  420)

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 1773 PHE cc_start: 0.7245 (m-80) cc_final: 0.6953 (m-80)
REVERT: B 1778 THR cc_start: 0.9305 (p) cc_final: 0.8975 (p)
REVERT: B 2028 MET cc_start: 0.0904 (tpp) cc_final: 0.0527 (tpp)
REVERT: H   34 MET cc_start: 0.5078 (tpp) cc_final: 0.4578 (mmm)
REVERT: H   72 ASP cc_start: 0.9169 (t0) cc_final: 0.8625 (p0)
REVERT: L    2 ILE cc_start: 0.5859 (mt) cc_final: 0.5550 (mt)
REVERT: L    3 VAL cc_start: 0.8802 (t) cc_final: 0.8538 (p)
REVERT: L   53 TYR cc_start: 0.9404 (m-80) cc_final: 0.8980 (m-10)
REVERT: L   55 TYR cc_start: 0.8439 (t80) cc_final: 0.8128 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0679
  time to fit residues: 6.9670
Evaluate side-chains
  43 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 36 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 19 optimal weight:    0.6980
   chunk 47 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 6 optimal weight:    9.9990
   chunk 9 optimal weight:    0.0270
   chunk 16 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 33 optimal weight:    8.9990
   overall best weight:    3.1444

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

Flipped N/Q/H residues before XYZ refinement:
** B1690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1774 HIS
** H  81 GLN ** 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 = 0.4378 r_free = 0.4378 target = 0.089082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.079030 restraints weight = 47226.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.081413 restraints weight = 47675.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.082712 restraints weight = 29334.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.082855 restraints weight = 23562.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.083269 restraints weight = 21235.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.4245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5338
moved from start:          0.5469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   4516  Z= 0.251
  Angle     :  0.825   9.788   6109  Z= 0.444
  Chirality :  0.048   0.161    670
  Planarity :  0.006   0.053    783
  Dihedral  :  6.649  23.137    595
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 22.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.35), residues: 551
  helix:  0.69 (0.92), residues: 35
  sheet:  0.39 (0.41), residues: 161
  loop : -1.18 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B1772 
 TYR   0.018   0.002   TYR B2007 
 PHE   0.030   0.003   PHE B1978 
 TRP   0.022   0.004   TRP H 103 
 HIS   0.005   0.001   HIS B1876 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 ( 4509)
  covalent geometry    : angle       0.82401 ( 6095)
  SS BOND              : bond        0.00402 (    7)
  SS BOND              : angle       1.04698 (   14)
  hydrogen bonds       : bond        0.04593 (  144)
  hydrogen bonds       : angle       6.92581 (  420)

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 1687 MET cc_start: 0.5362 (tpt) cc_final: 0.4384 (ppp)
REVERT: B 1773 PHE cc_start: 0.7710 (m-80) cc_final: 0.7081 (m-80)
REVERT: B 1775 ASN cc_start: 0.8829 (p0) cc_final: 0.8572 (p0)
REVERT: B 1778 THR cc_start: 0.9253 (p) cc_final: 0.8841 (p)
REVERT: B 1806 THR cc_start: 0.8438 (m) cc_final: 0.8234 (m)
REVERT: B 1971 ASP cc_start: 0.8530 (m-30) cc_final: 0.8325 (m-30)
REVERT: H   32 TYR cc_start: 0.7894 (m-10) cc_final: 0.7347 (m-10)
REVERT: H   34 MET cc_start: 0.5510 (tpp) cc_final: 0.5073 (mmm)
REVERT: L    3 VAL cc_start: 0.8822 (t) cc_final: 0.8552 (p)
REVERT: L   53 TYR cc_start: 0.9295 (m-80) cc_final: 0.8791 (m-10)
REVERT: L   55 TYR cc_start: 0.8079 (t80) cc_final: 0.7624 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0645
  time to fit residues: 5.5660
Evaluate side-chains
  37 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 26 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 48 optimal weight:    8.9990
   chunk 23 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 24 optimal weight:    0.2980
   chunk 38 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    5.2588

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

Flipped N/Q/H residues before XYZ refinement:
B1690 GLN
B1932 ASN
** B1994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B2033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.085214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.075101 restraints weight = 47372.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.077367 restraints weight = 45763.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.078141 restraints weight = 30140.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.078746 restraints weight = 23947.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.079030 restraints weight = 21162.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5525
moved from start:          0.7659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.079   4516  Z= 0.366
  Angle     :  1.065   9.741   6109  Z= 0.575
  Chirality :  0.054   0.252    670
  Planarity :  0.007   0.065    783
  Dihedral  :  8.303  34.898    595
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 37.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  4.20 %
    Favored  : 95.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -2.09 (0.33), residues: 551
  helix: -0.53 (0.80), residues: 44
  sheet: -0.56 (0.40), residues: 167
  loop : -2.03 (0.30), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG L  18 
 TYR   0.023   0.003   TYR B1892 
 PHE   0.024   0.003   PHE L  71 
 TRP   0.021   0.003   TRP H 103 
 HIS   0.009   0.002   HIS B1876 

Details of bonding type rmsd
  covalent geometry    : bond        0.00743 ( 4509)
  covalent geometry    : angle       1.06229 ( 6095)
  SS BOND              : bond        0.00611 (    7)
  SS BOND              : angle       1.92944 (   14)
  hydrogen bonds       : bond        0.06283 (  144)
  hydrogen bonds       : angle       8.33115 (  420)

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 1687 MET cc_start: 0.5510 (tpt) cc_final: 0.5170 (ppp)
REVERT: B 1775 ASN cc_start: 0.8962 (p0) cc_final: 0.8706 (p0)
REVERT: B 1932 ASN cc_start: 0.6921 (OUTLIER) cc_final: 0.6322 (t0)
REVERT: B 2028 MET cc_start: 0.1400 (tpp) cc_final: 0.0765 (tpp)
REVERT: L   53 TYR cc_start: 0.9245 (m-80) cc_final: 0.8687 (m-10)
REVERT: L   55 TYR cc_start: 0.7947 (t80) cc_final: 0.7746 (t80)
REVERT: L   65 SER cc_start: 0.8513 (t) cc_final: 0.8126 (m)
REVERT: L   82 ASP cc_start: 0.6740 (m-30) cc_final: 0.6243 (m-30)
REVERT: L   92 TYR cc_start: 0.8692 (t80) cc_final: 0.8287 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 57
  average time/residue: 0.0601
  time to fit residues: 4.5644
Evaluate side-chains
  36 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 35
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9980
   chunk 27 optimal weight:    0.1980
   chunk 35 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    3.4386

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

Flipped N/Q/H residues before XYZ refinement:
B1704 ASN
B1891 GLN
** H   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.085146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.075433 restraints weight = 47569.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.077784 restraints weight = 48080.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.078809 restraints weight = 27012.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.079110 restraints weight = 21111.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.079894 restraints weight = 18674.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5500
moved from start:          0.8011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   4516  Z= 0.244
  Angle     :  0.832   8.651   6109  Z= 0.456
  Chirality :  0.048   0.146    670
  Planarity :  0.007   0.133    783
  Dihedral  :  7.632  26.386    595
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 30.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.19 %
    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: -2.19 (0.34), residues: 551
  helix: -0.22 (0.84), residues: 44
  sheet: -0.81 (0.39), residues: 174
  loop : -2.08 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  13 
 TYR   0.028   0.002   TYR H  32 
 PHE   0.020   0.003   PHE B1978 
 TRP   0.031   0.004   TRP H 103 
 HIS   0.006   0.002   HIS B1876 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 4509)
  covalent geometry    : angle       0.83077 ( 6095)
  SS BOND              : bond        0.00393 (    7)
  SS BOND              : angle       1.32180 (   14)
  hydrogen bonds       : bond        0.04869 (  144)
  hydrogen bonds       : angle       7.86776 (  420)

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 1687 MET cc_start: 0.4969 (tpt) cc_final: 0.4695 (ppp)
REVERT: B 1745 ASP cc_start: 0.9056 (p0) cc_final: 0.8841 (p0)
REVERT: B 1773 PHE cc_start: 0.7185 (m-10) cc_final: 0.6466 (m-10)
REVERT: B 1775 ASN cc_start: 0.8919 (p0) cc_final: 0.8642 (p0)
REVERT: H   34 MET cc_start: 0.4717 (mmm) cc_final: 0.3370 (mmm)
REVERT: H  100 MET cc_start: 0.6546 (tpp) cc_final: 0.5745 (tpp)
REVERT: L   53 TYR cc_start: 0.9225 (m-80) cc_final: 0.8689 (m-10)
REVERT: L   65 SER cc_start: 0.8164 (t) cc_final: 0.7831 (m)
REVERT: L   82 ASP cc_start: 0.7054 (m-30) cc_final: 0.6446 (m-30)
REVERT: L   92 TYR cc_start: 0.8386 (t80) cc_final: 0.7931 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0592
  time to fit residues: 4.2193
Evaluate side-chains
  36 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 25 optimal weight:    6.9990
   chunk 41 optimal weight:    7.9990
   chunk 40 optimal weight:    0.7980
   chunk 8 optimal weight:    9.9990
   chunk 35 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 31 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    5.3588

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

Flipped N/Q/H residues before XYZ refinement:
B1704 ASN
** B1994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B2033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.082971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.073032 restraints weight = 47301.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.075069 restraints weight = 51094.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.074908 restraints weight = 40347.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.076139 restraints weight = 29462.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.076323 restraints weight = 23142.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5672
moved from start:          0.9288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.103   4516  Z= 0.357
  Angle     :  1.046  11.989   6109  Z= 0.570
  Chirality :  0.054   0.196    670
  Planarity :  0.008   0.103    783
  Dihedral  :  8.630  33.456    595
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 45.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.62 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -2.57 (0.34), residues: 551
  helix:  0.45 (0.88), residues: 37
  sheet: -1.26 (0.38), residues: 184
  loop : -2.32 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.002   ARG H  40 
 TYR   0.024   0.003   TYR H  91 
 PHE   0.035   0.003   PHE B1978 
 TRP   0.014   0.003   TRP H 103 
 HIS   0.010   0.002   HIS B1876 

Details of bonding type rmsd
  covalent geometry    : bond        0.00743 ( 4509)
  covalent geometry    : angle       1.04441 ( 6095)
  SS BOND              : bond        0.00716 (    7)
  SS BOND              : angle       1.58814 (   14)
  hydrogen bonds       : bond        0.05737 (  144)
  hydrogen bonds       : angle       8.66952 (  420)

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 1745 ASP cc_start: 0.9172 (p0) cc_final: 0.8880 (p0)
REVERT: B 1773 PHE cc_start: 0.7210 (m-10) cc_final: 0.6624 (m-10)
REVERT: B 1850 MET cc_start: 0.6365 (mmp) cc_final: 0.5849 (tpp)
REVERT: H   34 MET cc_start: 0.5498 (mmm) cc_final: 0.5010 (mmm)
REVERT: H  100 MET cc_start: 0.7090 (tpp) cc_final: 0.6880 (tpp)
REVERT: L   53 TYR cc_start: 0.9184 (m-80) cc_final: 0.8671 (m-10)
REVERT: L   65 SER cc_start: 0.8356 (t) cc_final: 0.8057 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0697
  time to fit residues: 4.2623
Evaluate side-chains
  33 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 10 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   chunk 32 optimal weight:    0.0040
   chunk 23 optimal weight:    0.9980
   overall best weight:    2.1998

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

Flipped N/Q/H residues before XYZ refinement:
B1704 ASN
B1891 GLN
** B1945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  89 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.084338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.074683 restraints weight = 47415.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.077104 restraints weight = 45548.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.078008 restraints weight = 25987.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.078432 restraints weight = 20431.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.079006 restraints weight = 18176.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.4165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5574
moved from start:          0.9188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   4516  Z= 0.204
  Angle     :  0.788   8.449   6109  Z= 0.435
  Chirality :  0.048   0.156    670
  Planarity :  0.006   0.074    783
  Dihedral  :  7.758  28.823    595
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 29.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.44 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.19 %
    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: -2.25 (0.35), residues: 551
  helix:  0.67 (0.90), residues: 38
  sheet: -1.19 (0.39), residues: 189
  loop : -2.01 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  40 
 TYR   0.024   0.002   TYR B2007 
 PHE   0.020   0.003   PHE B1978 
 TRP   0.020   0.003   TRP H 103 
 HIS   0.005   0.001   HIS B1965 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 4509)
  covalent geometry    : angle       0.78712 ( 6095)
  SS BOND              : bond        0.00336 (    7)
  SS BOND              : angle       1.20835 (   14)
  hydrogen bonds       : bond        0.04188 (  144)
  hydrogen bonds       : angle       7.71243 (  420)

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 1684 LYS cc_start: 0.9017 (tmmt) cc_final: 0.8724 (tmtt)
REVERT: B 1745 ASP cc_start: 0.9073 (p0) cc_final: 0.8809 (p0)
REVERT: B 1773 PHE cc_start: 0.7171 (m-10) cc_final: 0.6665 (m-10)
REVERT: B 1850 MET cc_start: 0.6066 (mmp) cc_final: 0.5514 (tpp)
REVERT: H   34 MET cc_start: 0.5024 (mmm) cc_final: 0.4550 (mmm)
REVERT: L   53 TYR cc_start: 0.9198 (m-80) cc_final: 0.8670 (m-10)
REVERT: L   55 TYR cc_start: 0.8055 (t80) cc_final: 0.7794 (t80)
REVERT: L   65 SER cc_start: 0.8210 (t) cc_final: 0.7882 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0531
  time to fit residues: 3.3305
Evaluate side-chains
  33 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0870
   chunk 40 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 14 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 50 optimal weight:    8.9990
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
H  43 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.086186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.076206 restraints weight = 47348.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.078579 restraints weight = 45903.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.079691 restraints weight = 28579.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.080041 restraints weight = 22099.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.080372 restraints weight = 20244.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5554
moved from start:          0.8970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4516  Z= 0.143
  Angle     :  0.714  15.683   6109  Z= 0.381
  Chirality :  0.047   0.255    670
  Planarity :  0.005   0.053    783
  Dihedral  :  6.799  29.795    595
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 19.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.19 %
    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: -1.84 (0.36), residues: 551
  helix:  0.99 (0.92), residues: 38
  sheet: -0.66 (0.40), residues: 177
  loop : -1.88 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  94 
 TYR   0.022   0.002   TYR B2007 
 PHE   0.020   0.002   PHE B1978 
 TRP   0.026   0.003   TRP H 103 
 HIS   0.004   0.001   HIS B1965 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 4509)
  covalent geometry    : angle       0.71252 ( 6095)
  SS BOND              : bond        0.00326 (    7)
  SS BOND              : angle       1.06005 (   14)
  hydrogen bonds       : bond        0.03445 (  144)
  hydrogen bonds       : angle       6.79046 (  420)

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 1687 MET cc_start: 0.5601 (ppp) cc_final: 0.5359 (ppp)
REVERT: B 1745 ASP cc_start: 0.9068 (p0) cc_final: 0.8860 (p0)
REVERT: B 1773 PHE cc_start: 0.7339 (m-10) cc_final: 0.6859 (m-10)
REVERT: B 2028 MET cc_start: 0.0060 (tpp) cc_final: -0.0788 (tpp)
REVERT: H    5 GLN cc_start: 0.8388 (tp-100) cc_final: 0.8079 (tm-30)
REVERT: H   34 MET cc_start: 0.4861 (mmm) cc_final: 0.3416 (mmm)
REVERT: L   53 TYR cc_start: 0.9186 (m-80) cc_final: 0.8653 (m-10)
REVERT: L   55 TYR cc_start: 0.7970 (t80) cc_final: 0.7762 (t80)
REVERT: L   65 SER cc_start: 0.7989 (t) cc_final: 0.7643 (m)
REVERT: L   82 ASP cc_start: 0.6886 (m-30) cc_final: 0.6456 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.0633
  time to fit residues: 4.6644
Evaluate side-chains
  36 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 43 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0060
   chunk 4 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 7 optimal weight:    9.9990
   chunk 34 optimal weight:    0.8980
   chunk 0 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 15 optimal weight:    9.9990
   overall best weight:    1.3798

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.085814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.075980 restraints weight = 47921.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.078259 restraints weight = 47403.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.079255 restraints weight = 29958.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.079672 restraints weight = 23293.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.080124 restraints weight = 21408.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.4194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5557
moved from start:          0.9150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4516  Z= 0.152
  Angle     :  0.720  10.958   6109  Z= 0.385
  Chirality :  0.047   0.166    670
  Planarity :  0.005   0.043    783
  Dihedral  :  6.698  26.014    595
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 21.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.19 %
    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: -1.80 (0.36), residues: 551
  helix:  0.80 (0.90), residues: 38
  sheet: -0.62 (0.41), residues: 170
  loop : -1.82 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  94 
 TYR   0.016   0.002   TYR B2007 
 PHE   0.018   0.002   PHE B1978 
 TRP   0.021   0.002   TRP H 103 
 HIS   0.004   0.001   HIS B1965 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4509)
  covalent geometry    : angle       0.71832 ( 6095)
  SS BOND              : bond        0.00369 (    7)
  SS BOND              : angle       1.17796 (   14)
  hydrogen bonds       : bond        0.03695 (  144)
  hydrogen bonds       : angle       6.78175 (  420)

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 1687 MET cc_start: 0.5638 (ppp) cc_final: 0.5371 (ppp)
REVERT: B 1773 PHE cc_start: 0.7378 (m-10) cc_final: 0.6980 (m-10)
REVERT: B 1850 MET cc_start: 0.5860 (mmp) cc_final: 0.5285 (tpp)
REVERT: B 1897 ASN cc_start: 0.9325 (m110) cc_final: 0.8802 (t0)
REVERT: H    3 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7854 (tm-30)
REVERT: H   34 MET cc_start: 0.5229 (mmm) cc_final: 0.4365 (mmm)
REVERT: L   53 TYR cc_start: 0.9210 (m-80) cc_final: 0.8682 (m-10)
REVERT: L   55 TYR cc_start: 0.7997 (t80) cc_final: 0.7755 (t80)
REVERT: L   82 ASP cc_start: 0.7037 (m-30) cc_final: 0.6617 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.0734
  time to fit residues: 5.1795
Evaluate side-chains
  36 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 14 optimal weight:    0.0870
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   overall best weight:    1.3762

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.085979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.076302 restraints weight = 48457.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.078552 restraints weight = 47952.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.079599 restraints weight = 30090.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.079898 restraints weight = 23309.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.080393 restraints weight = 21709.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.4207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5553
moved from start:          0.9288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4516  Z= 0.148
  Angle     :  0.711   9.388   6109  Z= 0.382
  Chirality :  0.047   0.204    670
  Planarity :  0.005   0.055    783
  Dihedral  :  6.616  24.771    595
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 19.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.19 %
    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: -1.82 (0.36), residues: 551
  helix:  0.80 (0.88), residues: 38
  sheet: -0.63 (0.39), residues: 177
  loop : -1.85 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG L  61 
 TYR   0.016   0.002   TYR B2007 
 PHE   0.018   0.002   PHE B1978 
 TRP   0.074   0.005   TRP H 103 
 HIS   0.004   0.001   HIS B1965 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 4509)
  covalent geometry    : angle       0.71015 ( 6095)
  SS BOND              : bond        0.00288 (    7)
  SS BOND              : angle       1.07879 (   14)
  hydrogen bonds       : bond        0.03638 (  144)
  hydrogen bonds       : angle       6.76203 (  420)

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

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

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1102 Ramachandran restraints generated.
    551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  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: B 1687 MET cc_start: 0.5599 (ppp) cc_final: 0.5345 (ppp)
REVERT: B 1773 PHE cc_start: 0.7433 (m-10) cc_final: 0.6872 (m-10)
REVERT: B 1855 LYS cc_start: 0.7123 (mmtt) cc_final: 0.5819 (ptpt)
REVERT: B 1897 ASN cc_start: 0.9320 (m110) cc_final: 0.8812 (t0)
REVERT: H   34 MET cc_start: 0.5305 (mmm) cc_final: 0.4924 (mmm)
REVERT: H  100 MET cc_start: 0.5910 (tpp) cc_final: 0.5515 (tpp)
REVERT: L   53 TYR cc_start: 0.9242 (m-80) cc_final: 0.8763 (m-10)
REVERT: L   55 TYR cc_start: 0.8109 (t80) cc_final: 0.7781 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0567
  time to fit residues: 3.7887
Evaluate side-chains
  38 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 33 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0040
   chunk 6 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 13 optimal weight:    0.5980
   chunk 2 optimal weight:    0.2980
   chunk 27 optimal weight:    0.4980
   chunk 1 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.0794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.086073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.076267 restraints weight = 48587.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.078604 restraints weight = 47845.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.079821 restraints weight = 29249.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.080138 restraints weight = 22419.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.080409 restraints weight = 20714.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.4210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5572
moved from start:          0.9350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4516  Z= 0.138
  Angle     :  0.687   8.758   6109  Z= 0.367
  Chirality :  0.046   0.163    670
  Planarity :  0.005   0.042    783
  Dihedral  :  6.327  24.061    595
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 17.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.19 %
    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: -1.82 (0.36), residues: 551
  helix:  0.82 (0.85), residues: 38
  sheet: -0.61 (0.40), residues: 167
  loop : -1.84 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG H  40 
 TYR   0.015   0.002   TYR B2007 
 PHE   0.018   0.002   PHE B1978 
 TRP   0.055   0.004   TRP H 103 
 HIS   0.004   0.001   HIS B1965 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4509)
  covalent geometry    : angle       0.68576 ( 6095)
  SS BOND              : bond        0.00285 (    7)
  SS BOND              : angle       1.04516 (   14)
  hydrogen bonds       : bond        0.03447 (  144)
  hydrogen bonds       : angle       6.56332 (  420)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 797.29 seconds
wall clock time: 14 minutes 36.58 seconds (876.58 seconds total)