Starting phenix.real_space_refine
on Thu Mar 13 17:10:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vlw_43346/03_2025/8vlw_43346.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vlw_43346/03_2025/8vlw_43346.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vlw_43346/03_2025/8vlw_43346.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vlw_43346/03_2025/8vlw_43346.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vlw_43346/03_2025/8vlw_43346.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vlw_43346/03_2025/8vlw_43346.cif"
  }
  resolution = 3.34
  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=   0.008
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      38      5.16       5
     C    5909      2.51       5
     N    1501      2.21       5
     O    1645      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9093
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1710
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 220, 1699
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 5, 'TRANS': 214}
      Conformer: "B"
        Number of residues, atoms: 220, 1699
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 5, 'TRANS': 214}
          bond proxies already assigned to first conformer: 1719
    Chain: "E"
      Number of atoms: 1693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1693
          Classifications: {'peptide': 219}
          Link IDs: {'PTRANS': 5, 'TRANS': 213}
    Chain: "D"
      Number of atoms: 1693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1693
          Classifications: {'peptide': 219}
          Link IDs: {'PTRANS': 5, 'TRANS': 213}
    Chain: "C"
      Number of atoms: 1699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1699
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 5, 'TRANS': 214}
    Chain: "B"
      Number of atoms: 1693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1693
          Classifications: {'peptide': 219}
          Link IDs: {'PTRANS': 5, 'TRANS': 213}
    Chain: "F"
      Number of atoms: 310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 310
          Classifications: {'peptide': 39}
          Link IDs: {'PTRANS': 3, 'TRANS': 35}
    Chain: "G"
      Number of atoms: 295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 295
          Classifications: {'peptide': 37}
          Link IDs: {'PTRANS': 3, 'TRANS': 33}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APHE A 146 " occ=0.76
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 146 " occ=0.24
  Time building chain proxies: 7.98, per 1000 atoms: 0.88
  Number of scatterers: 9093
  At special positions: 0
  Unit cell: (84.234, 88.404, 114.258, 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      38     16.00
     O    1645      8.00
     N    1501      7.00
     C    5909      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.46
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2186

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 0 sheets defined
      88.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 16
      removed outlier: 3.805A  pdb=" N   SER A  12 " --> pdb=" O   THR A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 62
    Processing helix  chain 'A' and resid 66 through 77
    Processing helix  chain 'A' and resid 82 through 100
      removed outlier: 3.510A  pdb=" N   ILE A  86 " --> pdb=" O   GLY A  82 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ARG A 100 " --> pdb=" O   LYS A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 127
    Processing helix  chain 'A' and resid 129 through 158
      Proline residue:  A 141  - end of helix
    Processing helix  chain 'A' and resid 166 through 226
      Proline residue:  A 172  - end of helix
      removed outlier: 3.540A  pdb=" N   ALA A 177 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ILE A 179 " --> pdb=" O   ALA A 175 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   ALA A 180 " --> pdb=" O   GLU A 176 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   THR A 181 " --> pdb=" O   ALA A 177 " (cutoff:3.500A)
      Proline residue:  A 190  - end of helix
      removed outlier: 3.642A  pdb=" N   VAL A 225 " --> pdb=" O   GLN A 221 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLY A 226 " --> pdb=" O   ARG A 222 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 9 through 16
      removed outlier: 4.114A  pdb=" N   LEU E  16 " --> pdb=" O   SER E  12 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 19 through 62
    Processing helix  chain 'E' and resid 66 through 77
    Processing helix  chain 'E' and resid 82 through 99
    Processing helix  chain 'E' and resid 103 through 127
    Processing helix  chain 'E' and resid 129 through 160
      Proline residue:  E 141  - end of helix
    Processing helix  chain 'E' and resid 170 through 226
      removed outlier: 3.575A  pdb=" N   ILE E 174 " --> pdb=" O   VAL E 170 " (cutoff:3.500A)
      Proline residue:  E 190  - end of helix
      removed outlier: 3.741A  pdb=" N   GLY E 226 " --> pdb=" O   ARG E 222 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 10 through 17
      removed outlier: 3.946A  pdb=" N   GLN D  17 " --> pdb=" O   ASP D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 62
    Processing helix  chain 'D' and resid 66 through 77
    Processing helix  chain 'D' and resid 82 through 99
    Processing helix  chain 'D' and resid 103 through 127
      removed outlier: 3.512A  pdb=" N   MET D 107 " --> pdb=" O   PRO D 103 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 159
      Proline residue:  D 141  - end of helix
    Processing helix  chain 'D' and resid 166 through 226
      Proline residue:  D 172  - end of helix
      removed outlier: 3.505A  pdb=" N   GLU D 176 " --> pdb=" O   PRO D 172 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ALA D 180 " --> pdb=" O   GLU D 176 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   THR D 181 " --> pdb=" O   ALA D 177 " (cutoff:3.500A)
      Proline residue:  D 190  - end of helix
      removed outlier: 3.778A  pdb=" N   GLY D 226 " --> pdb=" O   ARG D 222 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 17
    Processing helix  chain 'C' and resid 19 through 62
    Processing helix  chain 'C' and resid 66 through 77
    Processing helix  chain 'C' and resid 82 through 97
      removed outlier: 3.868A  pdb=" N   SER C  92 " --> pdb=" O   TYR C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 127
    Processing helix  chain 'C' and resid 129 through 162
      Proline residue:  C 141  - end of helix
    Processing helix  chain 'C' and resid 166 through 226
      Proline residue:  C 172  - end of helix
      Proline residue:  C 190  - end of helix
    Processing helix  chain 'B' and resid 10 through 17
    Processing helix  chain 'B' and resid 19 through 62
    Processing helix  chain 'B' and resid 66 through 77
    Processing helix  chain 'B' and resid 82 through 100
      removed outlier: 3.942A  pdb=" N   ARG B 100 " --> pdb=" O   LYS B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 127
    Processing helix  chain 'B' and resid 129 through 160
      Proline residue:  B 141  - end of helix
    Processing helix  chain 'B' and resid 170 through 187
      removed outlier: 3.828A  pdb=" N   THR B 181 " --> pdb=" O   ALA B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 226
      removed outlier: 3.587A  pdb=" N   GLY B 226 " --> pdb=" O   ARG B 222 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 44
      Proline residue:  F  41  - end of helix
    Processing helix  chain 'G' and resid 24 through 40
    Processing helix  chain 'G' and resid 41 through 43
      No H-bonds generated for 'chain 'G' and resid 41 through 43'

    818 hydrogen bonds defined for protein.
    2455 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: 3.07

  Time building geometry restraints manager: 2.89 seconds

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

  Histogram of bond lengths:
        1.17 -     1.31: 1538
        1.31 -     1.44: 2362
        1.44 -     1.58: 5294
        1.58 -     1.71: 0
        1.71 -     1.85: 76
  Bond restraints: 9270
  Sorted by residual:
  bond pdb=" C   ALA B 177 "
       pdb=" O   ALA B 177 "
    ideal  model  delta    sigma   weight residual
    1.236  1.178  0.058 1.25e-02 6.40e+03 2.17e+01
  bond pdb=" C   GLU D 127 "
       pdb=" O   GLU D 127 "
    ideal  model  delta    sigma   weight residual
    1.234  1.286 -0.052 1.14e-02 7.69e+03 2.10e+01
  bond pdb=" C   GLY A 158 "
       pdb=" O   GLY A 158 "
    ideal  model  delta    sigma   weight residual
    1.236  1.174  0.061 1.35e-02 5.49e+03 2.06e+01
  bond pdb=" C   ALA B  74 "
       pdb=" O   ALA B  74 "
    ideal  model  delta    sigma   weight residual
    1.237  1.290 -0.054 1.19e-02 7.06e+03 2.04e+01
  bond pdb=" C   GLN D  58 "
       pdb=" O   GLN D  58 "
    ideal  model  delta    sigma   weight residual
    1.236  1.287 -0.050 1.15e-02 7.56e+03 1.92e+01
  ... (remaining 9265 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 10712
        1.67 -     3.34: 1623
        3.34 -     5.01: 176
        5.01 -     6.68: 31
        6.68 -     8.35: 9
  Bond angle restraints: 12551
  Sorted by residual:
  angle pdb=" CA  ASP D  53 "
        pdb=" CB  ASP D  53 "
        pdb=" CG  ASP D  53 "
      ideal   model   delta    sigma   weight residual
     112.60  116.85   -4.25 1.00e+00 1.00e+00 1.81e+01
  angle pdb=" CA  ASP D 208 "
        pdb=" CB  ASP D 208 "
        pdb=" CG  ASP D 208 "
      ideal   model   delta    sigma   weight residual
     112.60  116.74   -4.14 1.00e+00 1.00e+00 1.72e+01
  angle pdb=" CA  PHE D 212 "
        pdb=" CB  PHE D 212 "
        pdb=" CG  PHE D 212 "
      ideal   model   delta    sigma   weight residual
     113.80  109.77    4.03 1.00e+00 1.00e+00 1.62e+01
  angle pdb=" CA  ASP C 208 "
        pdb=" CB  ASP C 208 "
        pdb=" CG  ASP C 208 "
      ideal   model   delta    sigma   weight residual
     112.60  116.58   -3.98 1.00e+00 1.00e+00 1.58e+01
  angle pdb=" CB  GLU B 203 "
        pdb=" CG  GLU B 203 "
        pdb=" CD  GLU B 203 "
      ideal   model   delta    sigma   weight residual
     112.60  119.34   -6.74 1.70e+00 3.46e-01 1.57e+01
  ... (remaining 12546 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 4896
       17.64 -    35.29: 497
       35.29 -    52.93: 97
       52.93 -    70.58: 11
       70.58 -    88.22: 7
  Dihedral angle restraints: 5508
    sinusoidal: 2117
      harmonic: 3391
  Sorted by residual:
  dihedral pdb=" CA  ALA A 161 "
           pdb=" C   ALA A 161 "
           pdb=" N   VAL A 162 "
           pdb=" CA  VAL A 162 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.14  -28.86     0      5.00e+00 4.00e-02 3.33e+01
  dihedral pdb=" CA  ALA A 160 "
           pdb=" C   ALA A 160 "
           pdb=" N   ALA A 161 "
           pdb=" CA  ALA A 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.27   24.73     0      5.00e+00 4.00e-02 2.45e+01
  dihedral pdb=" CA  ASP A 163 "
           pdb=" C   ASP A 163 "
           pdb=" N   GLN A 164 "
           pdb=" CA  GLN A 164 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.36   18.64     0      5.00e+00 4.00e-02 1.39e+01
  ... (remaining 5505 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 863
       0.063 -    0.125: 430
       0.125 -    0.187: 139
       0.187 -    0.250: 29
       0.250 -    0.312: 9
  Chirality restraints: 1470
  Sorted by residual:
  chirality pdb=" CA  PRO A 172 "
            pdb=" N   PRO A 172 "
            pdb=" C   PRO A 172 "
            pdb=" CB  PRO A 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.41    0.31 2.00e-01 2.50e+01 2.44e+00
  chirality pdb=" CA  PRO C  20 "
            pdb=" N   PRO C  20 "
            pdb=" C   PRO C  20 "
            pdb=" CB  PRO C  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.45    0.27 2.00e-01 2.50e+01 1.78e+00
  chirality pdb=" CB  VAL E 170 "
            pdb=" CA  VAL E 170 "
            pdb=" CG1 VAL E 170 "
            pdb=" CG2 VAL E 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.77e+00
  ... (remaining 1467 not shown)

  Planarity restraints: 1567
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  35 "   -0.012 2.00e-02 2.50e+03   2.80e-02 1.37e+01
        pdb=" CG  PHE C  35 "    0.057 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  35 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  35 "   -0.038 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  35 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  35 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  35 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 198 "    0.000 2.00e-02 2.50e+03   2.51e-02 1.10e+01
        pdb=" CG  PHE C 198 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 198 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 198 "    0.031 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 198 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 198 "   -0.028 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 198 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C  84 "   -0.016 2.00e-02 2.50e+03   3.32e-02 1.10e+01
        pdb=" C   GLU C  84 "    0.057 2.00e-02 2.50e+03
        pdb=" O   GLU C  84 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ASP C  85 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1564 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 500
        2.74 -     3.28: 10116
        3.28 -     3.82: 15444
        3.82 -     4.36: 16531
        4.36 -     4.90: 29169
  Nonbonded interactions: 71760
  Sorted by model distance:
  nonbonded pdb=" O   GLU E  66 "
            pdb=" OG1 THR E  69 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" N   GLN B 164 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" O   GLU B  66 "
            pdb=" OG1 THR B  69 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O   GLU D  66 "
            pdb=" OG1 THR D  69 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" O   LYS D  96 "
            pdb=" NZ  LYS D  96 "
     model   vdw
     2.370 3.120
  ... (remaining 71755 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 8 through 145 or resid 147 through 226))
  selection = (chain 'B' and (resid 8 through 145 or resid 147 through 226))
  selection = (chain 'C' and (resid 8 through 145 or resid 147 through 226))
  selection = (chain 'D' and (resid 8 through 145 or resid 147 through 226))
  selection = (chain 'E' and (resid 8 through 145 or resid 147 through 226))
}
ncs_group {
  reference = (chain 'F' and resid 9 through 45)
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.24 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             218.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.500
  Find NCS groups from input model:        0.480
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:3.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  249.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
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      :  0.013   0.091   9270  Z= 0.864
  Angle     :  1.223   8.348  12551  Z= 0.811
  Chirality :  0.080   0.312   1470
  Planarity :  0.009   0.061   1567
  Dihedral  : 14.549  88.222   3322
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.16 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.77 %
    Favored  : 98.13 %
  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:  1.74 (0.24), residues: 1162
  helix:  1.65 (0.16), residues: 1007
  sheet:  None (None), residues: 0
  loop : -2.07 (0.46), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.009   TRP B 150 
 HIS   0.039   0.009   HIS E  44 
 PHE   0.057   0.010   PHE C  35 
 TYR   0.047   0.009   TYR C 206 
 ARG   0.023   0.004   ARG A 222 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 219
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  208 ASP cc_start: 0.8803 (t0) cc_final: 0.8421 (t0)
REVERT: E   54 ASP cc_start: 0.8706 (t70) cc_final: 0.8480 (t0)
REVERT: D   60 MET cc_start: 0.9285 (tpp) cc_final: 0.8973 (tpp)
REVERT: D  100 ARG cc_start: 0.8329 (mmp80) cc_final: 0.8059 (mmp80)
REVERT: C   88 TYR cc_start: 0.8207 (t80) cc_final: 0.7800 (t80)
REVERT: C  109 GLU cc_start: 0.8676 (tp30) cc_final: 0.8454 (tp30)
REVERT: C  142 TYR cc_start: 0.7463 (m-80) cc_final: 0.6798 (m-80)
REVERT: C  176 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8178 (mt-10)
REVERT: B   42 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8615 (tttt)
REVERT: B  208 ASP cc_start: 0.8453 (t0) cc_final: 0.8150 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 220
  average time/residue: 0.2769
  time to fit residues: 77.7937
Evaluate side-chains
  160 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    0.6980
   chunk 85 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 88 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 102 optimal weight:    0.2980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** E  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 106 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 = 0.3318 r_free = 0.3318 target = 0.071517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.053065 restraints weight = 55669.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 4.96
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2876
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2876
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9270  Z= 0.218
  Angle     :  0.630   7.395  12551  Z= 0.317
  Chirality :  0.038   0.162   1470
  Planarity :  0.005   0.054   1567
  Dihedral  :  3.793  27.659   1248
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  1.47 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 10.09 %
    Favored  : 88.97 %
  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:  2.93 (0.25), residues: 1162
  helix:  2.43 (0.16), residues: 1023
  sheet:  None (None), residues: 0
  loop : -2.02 (0.50), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 150 
 HIS   0.004   0.001   HIS E  56 
 PHE   0.024   0.002   PHE D 212 
 TYR   0.011   0.001   TYR B  38 
 ARG   0.007   0.001   ARG E 113 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 177
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.8650 (t0) cc_final: 0.8389 (t0)
REVERT: A  208 ASP cc_start: 0.8835 (t0) cc_final: 0.8448 (t0)
REVERT: E   26 MET cc_start: 0.8570 (mtm) cc_final: 0.8044 (mtm)
REVERT: E   54 ASP cc_start: 0.8639 (t70) cc_final: 0.8405 (t0)
REVERT: E  208 ASP cc_start: 0.8323 (t0) cc_final: 0.8071 (t0)
REVERT: D   60 MET cc_start: 0.9470 (tpp) cc_final: 0.9061 (tpp)
REVERT: D  154 ASN cc_start: 0.8979 (t0) cc_final: 0.8584 (t0)
REVERT: D  197 HIS cc_start: 0.8432 (t-90) cc_final: 0.8210 (t-170)
REVERT: D  208 ASP cc_start: 0.8575 (t0) cc_final: 0.8333 (t0)
REVERT: C   59 LYS cc_start: 0.9367 (pptt) cc_final: 0.9103 (pptt)
REVERT: C   88 TYR cc_start: 0.8244 (t80) cc_final: 0.7741 (t80)
REVERT: C   99 LYS cc_start: 0.9460 (tppt) cc_final: 0.8903 (mmtm)
REVERT: C  116 ARG cc_start: 0.8737 (ttp80) cc_final: 0.8328 (ttp-110)
REVERT: C  142 TYR cc_start: 0.6901 (m-80) cc_final: 0.6401 (m-80)
REVERT: B   42 LYS cc_start: 0.8792 (ttpt) cc_final: 0.8464 (tttt)
REVERT: B   54 ASP cc_start: 0.8537 (t0) cc_final: 0.8274 (t0)
REVERT: B  109 GLU cc_start: 0.8468 (tt0) cc_final: 0.8257 (tt0)
REVERT: B  208 ASP cc_start: 0.8609 (t0) cc_final: 0.8238 (t0)
  outliers start: 9
  outliers final: 8
  residues processed: 185
  average time/residue: 0.3123
  time to fit residues: 73.0637
Evaluate side-chains
  173 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 165
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  217 ILE
Chi-restraints excluded: chain C residue   45 MET
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain G residue   43 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 112 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 70 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 97 optimal weight:    0.5980
   chunk 106 optimal weight:    2.9990
   chunk 6 optimal weight:    0.3980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** E  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 106 GLN
** C 106 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 = 0.3282 r_free = 0.3282 target = 0.070633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.051653 restraints weight = 56146.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.2835 rms_B_bonded: 5.17
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2837
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2837
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9270  Z= 0.204
  Angle     :  0.577   7.310  12551  Z= 0.288
  Chirality :  0.036   0.155   1470
  Planarity :  0.004   0.048   1567
  Dihedral  :  3.570  26.287   1248
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  1.98 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 12.07 %
    Favored  : 86.58 %
  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:  3.47 (0.25), residues: 1162
  helix:  2.78 (0.16), residues: 1024
  sheet:  None (None), residues: 0
  loop : -1.84 (0.51), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 150 
 HIS   0.003   0.000   HIS E  56 
 PHE   0.018   0.001   PHE D 212 
 TYR   0.009   0.001   TYR B 206 
 ARG   0.007   0.001   ARG E 113 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 176
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.8631 (t0) cc_final: 0.8403 (t0)
REVERT: A  154 ASN cc_start: 0.9114 (t0) cc_final: 0.8687 (m-40)
REVERT: A  208 ASP cc_start: 0.8838 (t0) cc_final: 0.8435 (t0)
REVERT: E   49 LYS cc_start: 0.9183 (tptp) cc_final: 0.8897 (tppt)
REVERT: E   96 LYS cc_start: 0.9411 (mmmt) cc_final: 0.9137 (mtmm)
REVERT: E  208 ASP cc_start: 0.8434 (t0) cc_final: 0.8132 (t0)
REVERT: D   59 LYS cc_start: 0.9119 (mmmt) cc_final: 0.8862 (ttpp)
REVERT: D   60 MET cc_start: 0.9500 (tpp) cc_final: 0.9059 (tpp)
REVERT: D   96 LYS cc_start: 0.9665 (tppp) cc_final: 0.9312 (tptp)
REVERT: D  113 ARG cc_start: 0.8496 (mmp80) cc_final: 0.8295 (mmp80)
REVERT: D  154 ASN cc_start: 0.8938 (t0) cc_final: 0.8620 (t0)
REVERT: D  208 ASP cc_start: 0.8686 (t0) cc_final: 0.8312 (t0)
REVERT: C   59 LYS cc_start: 0.9371 (pptt) cc_final: 0.9094 (pptt)
REVERT: C   88 TYR cc_start: 0.8276 (t80) cc_final: 0.7708 (t80)
REVERT: C   91 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8457 (tt)
REVERT: C   99 LYS cc_start: 0.9488 (tppt) cc_final: 0.8983 (mmtm)
REVERT: C  116 ARG cc_start: 0.8750 (ttp80) cc_final: 0.8278 (ttp-110)
REVERT: C  142 TYR cc_start: 0.6929 (m-80) cc_final: 0.6396 (m-80)
REVERT: B   42 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8408 (ttpt)
REVERT: B   93 GLU cc_start: 0.9226 (tp30) cc_final: 0.8975 (tp30)
REVERT: B  109 GLU cc_start: 0.8475 (tt0) cc_final: 0.8237 (tt0)
REVERT: B  122 ASP cc_start: 0.8874 (t0) cc_final: 0.8447 (t0)
REVERT: B  208 ASP cc_start: 0.8660 (t0) cc_final: 0.8282 (t0)
REVERT: F   13 LYS cc_start: 0.8565 (pttp) cc_final: 0.7953 (pptt)
REVERT: G   42 MET cc_start: 0.8783 (mtp) cc_final: 0.8316 (ttm)
  outliers start: 13
  outliers final: 5
  residues processed: 186
  average time/residue: 0.2931
  time to fit residues: 69.4610
Evaluate side-chains
  171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 165
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain D residue  217 ILE
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain G residue   43 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 102 optimal weight:    0.4980
   chunk 86 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0980
   chunk 74 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** E  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 106 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 = 0.3283 r_free = 0.3283 target = 0.070641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.052132 restraints weight = 42568.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 4.56
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9270  Z= 0.202
  Angle     :  0.560   6.872  12551  Z= 0.280
  Chirality :  0.036   0.152   1470
  Planarity :  0.004   0.046   1567
  Dihedral  :  3.420  23.097   1248
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  1.73 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.46 %
    Favored  : 83.56 %
  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:  3.72 (0.25), residues: 1162
  helix:  2.95 (0.16), residues: 1023
  sheet:  None (None), residues: 0
  loop : -1.77 (0.51), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 150 
 HIS   0.003   0.000   HIS E  56 
 PHE   0.015   0.001   PHE D 212 
 TYR   0.012   0.001   TYR G  25 
 ARG   0.008   0.001   ARG E 113 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 175
  time to evaluate  : 1.037 
Fit side-chains
REVERT: A   54 ASP cc_start: 0.8648 (t0) cc_final: 0.8447 (t0)
REVERT: A  154 ASN cc_start: 0.9085 (t0) cc_final: 0.8656 (m-40)
REVERT: A  208 ASP cc_start: 0.8870 (t0) cc_final: 0.8449 (t0)
REVERT: E   49 LYS cc_start: 0.9212 (tptp) cc_final: 0.8893 (tppt)
REVERT: E   96 LYS cc_start: 0.9376 (mmmt) cc_final: 0.9040 (mtmm)
REVERT: E  208 ASP cc_start: 0.8406 (t0) cc_final: 0.8148 (t0)
REVERT: D   13 ASP cc_start: 0.9520 (m-30) cc_final: 0.8852 (t0)
REVERT: D   59 LYS cc_start: 0.9133 (mmmt) cc_final: 0.8839 (ttpp)
REVERT: D   60 MET cc_start: 0.9478 (tpp) cc_final: 0.9014 (tpp)
REVERT: D   96 LYS cc_start: 0.9645 (tppp) cc_final: 0.9296 (tptp)
REVERT: D  154 ASN cc_start: 0.8952 (t0) cc_final: 0.8643 (t0)
REVERT: D  208 ASP cc_start: 0.8723 (t0) cc_final: 0.8323 (t0)
REVERT: C   59 LYS cc_start: 0.9356 (pptt) cc_final: 0.9071 (pptt)
REVERT: C   99 LYS cc_start: 0.9480 (tppt) cc_final: 0.8940 (mmtm)
REVERT: C  116 ARG cc_start: 0.8705 (ttp80) cc_final: 0.8321 (ttp-110)
REVERT: C  142 TYR cc_start: 0.6968 (m-80) cc_final: 0.6384 (m-80)
REVERT: B   42 LYS cc_start: 0.8750 (ttpt) cc_final: 0.8418 (ttpt)
REVERT: B  122 ASP cc_start: 0.8876 (t0) cc_final: 0.8429 (t0)
REVERT: B  208 ASP cc_start: 0.8658 (t0) cc_final: 0.8294 (t0)
REVERT: F   13 LYS cc_start: 0.8604 (pttp) cc_final: 0.8025 (pptt)
REVERT: G   42 MET cc_start: 0.8796 (mtp) cc_final: 0.8306 (ttm)
  outliers start: 19
  outliers final: 9
  residues processed: 187
  average time/residue: 0.3082
  time to fit residues: 72.8163
Evaluate side-chains
  172 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 163
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  163 ASP
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain G residue   43 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 27 optimal weight:    0.5980
   chunk 45 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 108 optimal weight:    4.9990
   chunk 38 optimal weight:    0.3980
   chunk 99 optimal weight:    0.7980
   chunk 88 optimal weight:    0.5980
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** E  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 106 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 = 0.3287 r_free = 0.3287 target = 0.070935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.051928 restraints weight = 46464.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 4.79
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2841
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9270  Z= 0.208
  Angle     :  0.562   7.483  12551  Z= 0.280
  Chirality :  0.036   0.155   1470
  Planarity :  0.004   0.046   1567
  Dihedral  :  3.366  21.935   1248
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.47 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.09 %
    Favored  : 82.93 %
  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:  3.88 (0.25), residues: 1162
  helix:  3.04 (0.16), residues: 1025
  sheet:  None (None), residues: 0
  loop : -1.63 (0.52), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 150 
 HIS   0.003   0.000   HIS E  56 
 PHE   0.015   0.001   PHE D 212 
 TYR   0.012   0.001   TYR C  71 
 ARG   0.009   0.001   ARG E 113 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 171
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 MET cc_start: 0.8836 (mtm) cc_final: 0.8596 (mpp)
REVERT: A  154 ASN cc_start: 0.9125 (t0) cc_final: 0.8683 (m-40)
REVERT: A  208 ASP cc_start: 0.8894 (t0) cc_final: 0.8473 (t0)
REVERT: E   26 MET cc_start: 0.8549 (mtm) cc_final: 0.7877 (mtm)
REVERT: E   49 LYS cc_start: 0.9201 (tptp) cc_final: 0.8864 (tppt)
REVERT: E  208 ASP cc_start: 0.8502 (t0) cc_final: 0.8216 (t0)
REVERT: D   13 ASP cc_start: 0.9503 (m-30) cc_final: 0.8870 (t0)
REVERT: D   54 ASP cc_start: 0.9089 (t0) cc_final: 0.8878 (t0)
REVERT: D   59 LYS cc_start: 0.9154 (mmmt) cc_final: 0.8857 (ttpp)
REVERT: D   60 MET cc_start: 0.9461 (tpp) cc_final: 0.8992 (tpp)
REVERT: D   96 LYS cc_start: 0.9627 (tppp) cc_final: 0.9291 (tptp)
REVERT: D  113 ARG cc_start: 0.8494 (mmp80) cc_final: 0.8232 (mmp80)
REVERT: D  153 MET cc_start: 0.8547 (mmm) cc_final: 0.8194 (tpp)
REVERT: D  197 HIS cc_start: 0.8396 (t-90) cc_final: 0.8185 (t-170)
REVERT: D  208 ASP cc_start: 0.8758 (t0) cc_final: 0.8349 (t0)
REVERT: C   35 PHE cc_start: 0.8466 (t80) cc_final: 0.8215 (t80)
REVERT: C   59 LYS cc_start: 0.9377 (pptt) cc_final: 0.9090 (pptt)
REVERT: C   99 LYS cc_start: 0.9485 (tppt) cc_final: 0.8949 (mmtm)
REVERT: C  116 ARG cc_start: 0.8773 (ttp80) cc_final: 0.8406 (ttp-110)
REVERT: C  142 TYR cc_start: 0.6997 (m-80) cc_final: 0.6368 (m-80)
REVERT: B   42 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8430 (ttpt)
REVERT: B  112 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8127 (tt0)
REVERT: B  122 ASP cc_start: 0.8889 (t0) cc_final: 0.8424 (t0)
REVERT: B  208 ASP cc_start: 0.8680 (t0) cc_final: 0.8320 (t0)
REVERT: F   13 LYS cc_start: 0.8606 (pttp) cc_final: 0.8043 (pptt)
REVERT: G   42 MET cc_start: 0.8806 (mtp) cc_final: 0.8322 (ttm)
  outliers start: 19
  outliers final: 8
  residues processed: 184
  average time/residue: 0.2876
  time to fit residues: 67.6350
Evaluate side-chains
  173 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 164
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  163 ASP
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain B residue  112 GLU
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain G residue   43 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 84 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 95 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** E  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  10 HIS
** C 106 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 = 0.3265 r_free = 0.3265 target = 0.069797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.051318 restraints weight = 46082.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.2829 rms_B_bonded: 4.70
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2831
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9270  Z= 0.229
  Angle     :  0.570   7.408  12551  Z= 0.286
  Chirality :  0.036   0.147   1470
  Planarity :  0.004   0.048   1567
  Dihedral  :  3.348  20.834   1248
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.64 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.82 %
    Favored  : 82.00 %
  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:  3.90 (0.25), residues: 1162
  helix:  3.05 (0.16), residues: 1025
  sheet:  None (None), residues: 0
  loop : -1.57 (0.52), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 150 
 HIS   0.003   0.001   HIS E  56 
 PHE   0.014   0.001   PHE A  57 
 TYR   0.016   0.001   TYR C  71 
 ARG   0.010   0.001   ARG F   8 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 169
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.8683 (t0) cc_final: 0.8423 (t0)
REVERT: A  154 ASN cc_start: 0.9128 (t0) cc_final: 0.8661 (m-40)
REVERT: A  208 ASP cc_start: 0.8846 (t0) cc_final: 0.8451 (t0)
REVERT: E   49 LYS cc_start: 0.9223 (tptp) cc_final: 0.8876 (tppt)
REVERT: E  208 ASP cc_start: 0.8486 (t0) cc_final: 0.8178 (t0)
REVERT: D   13 ASP cc_start: 0.9499 (m-30) cc_final: 0.8870 (t0)
REVERT: D   60 MET cc_start: 0.9465 (tpp) cc_final: 0.9054 (tpp)
REVERT: D   96 LYS cc_start: 0.9624 (tppp) cc_final: 0.9304 (tptp)
REVERT: D  197 HIS cc_start: 0.8452 (t-90) cc_final: 0.8227 (t-170)
REVERT: D  208 ASP cc_start: 0.8773 (t0) cc_final: 0.8386 (t0)
REVERT: C   16 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8858 (mt)
REVERT: C   35 PHE cc_start: 0.8416 (t80) cc_final: 0.8180 (t80)
REVERT: C   59 LYS cc_start: 0.9344 (pptt) cc_final: 0.9050 (pptt)
REVERT: C   99 LYS cc_start: 0.9494 (tppt) cc_final: 0.8952 (mmtm)
REVERT: C  116 ARG cc_start: 0.8757 (ttp80) cc_final: 0.8367 (ttp-110)
REVERT: C  142 TYR cc_start: 0.6940 (m-80) cc_final: 0.6343 (m-80)
REVERT: B   42 LYS cc_start: 0.8748 (ttpt) cc_final: 0.8442 (ttpt)
REVERT: B  109 GLU cc_start: 0.8504 (tt0) cc_final: 0.8217 (tt0)
REVERT: B  122 ASP cc_start: 0.8879 (t0) cc_final: 0.8413 (t0)
REVERT: B  208 ASP cc_start: 0.8696 (t0) cc_final: 0.8348 (t0)
REVERT: F   13 LYS cc_start: 0.8622 (pttp) cc_final: 0.8039 (pptt)
  outliers start: 21
  outliers final: 13
  residues processed: 182
  average time/residue: 0.3018
  time to fit residues: 69.8478
Evaluate side-chains
  176 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 162
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain C residue   10 HIS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  163 ASP
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain G residue   43 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 99 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 100 optimal weight:    0.2980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** E  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 106 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 = 0.3268 r_free = 0.3268 target = 0.069940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.051262 restraints weight = 48485.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 4.85
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2840
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9270  Z= 0.228
  Angle     :  0.578   9.095  12551  Z= 0.287
  Chirality :  0.036   0.143   1470
  Planarity :  0.004   0.052   1567
  Dihedral  :  3.294  19.748   1248
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.73 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 16.86 %
    Favored  : 81.48 %
  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:  3.99 (0.25), residues: 1162
  helix:  3.11 (0.16), residues: 1025
  sheet:  None (None), residues: 0
  loop : -1.54 (0.53), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 150 
 HIS   0.002   0.000   HIS A 197 
 PHE   0.013   0.001   PHE A  57 
 TYR   0.010   0.001   TYR F  25 
 ARG   0.010   0.001   ARG E 113 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 170
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.8672 (t0) cc_final: 0.8403 (t0)
REVERT: A   59 LYS cc_start: 0.9061 (tmmt) cc_final: 0.8858 (tmtt)
REVERT: A  154 ASN cc_start: 0.9159 (t0) cc_final: 0.8681 (m-40)
REVERT: A  208 ASP cc_start: 0.8834 (t0) cc_final: 0.8424 (t0)
REVERT: E  208 ASP cc_start: 0.8467 (t0) cc_final: 0.8185 (t0)
REVERT: D   13 ASP cc_start: 0.9494 (m-30) cc_final: 0.8863 (t0)
REVERT: D   59 LYS cc_start: 0.9203 (tppt) cc_final: 0.8854 (ttpp)
REVERT: D   60 MET cc_start: 0.9454 (tpp) cc_final: 0.9012 (tpp)
REVERT: D   96 LYS cc_start: 0.9599 (tppp) cc_final: 0.9289 (tptp)
REVERT: D  100 ARG cc_start: 0.8709 (mmp80) cc_final: 0.8253 (mmp80)
REVERT: D  113 ARG cc_start: 0.8474 (mmp80) cc_final: 0.8260 (mmp80)
REVERT: D  197 HIS cc_start: 0.8448 (t-90) cc_final: 0.8235 (t-170)
REVERT: D  208 ASP cc_start: 0.8777 (t0) cc_final: 0.8386 (t0)
REVERT: C   16 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8883 (mt)
REVERT: C   35 PHE cc_start: 0.8448 (t80) cc_final: 0.8191 (t80)
REVERT: C   59 LYS cc_start: 0.9349 (pptt) cc_final: 0.9057 (pptt)
REVERT: C   99 LYS cc_start: 0.9502 (tppt) cc_final: 0.8935 (mmtm)
REVERT: C  116 ARG cc_start: 0.8823 (ttp80) cc_final: 0.8370 (ttp-110)
REVERT: C  142 TYR cc_start: 0.6963 (m-80) cc_final: 0.6349 (m-80)
REVERT: B   42 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8432 (ttpt)
REVERT: B  109 GLU cc_start: 0.8453 (tt0) cc_final: 0.8235 (tt0)
REVERT: B  112 GLU cc_start: 0.8755 (tt0) cc_final: 0.8529 (tt0)
REVERT: B  122 ASP cc_start: 0.8869 (t0) cc_final: 0.8405 (t0)
REVERT: B  208 ASP cc_start: 0.8708 (t0) cc_final: 0.8356 (t0)
REVERT: F   13 LYS cc_start: 0.8605 (pttp) cc_final: 0.8009 (pptt)
  outliers start: 16
  outliers final: 13
  residues processed: 181
  average time/residue: 0.3032
  time to fit residues: 69.5892
Evaluate side-chains
  176 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 162
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain C residue   10 HIS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  163 ASP
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain G residue   43 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 86 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** E  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  23 GLN
** C 106 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 = 0.3270 r_free = 0.3270 target = 0.070070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.050485 restraints weight = 63858.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 5.45
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2814
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2814 r_free = 0.2814    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2814 r_free = 0.2814    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2814
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9270  Z= 0.240
  Angle     :  0.587   7.844  12551  Z= 0.292
  Chirality :  0.036   0.141   1470
  Planarity :  0.004   0.059   1567
  Dihedral  :  3.270  18.998   1248
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.73 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.38 %
    Favored  : 80.75 %
  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:  3.94 (0.25), residues: 1162
  helix:  3.07 (0.16), residues: 1027
  sheet:  None (None), residues: 0
  loop : -1.57 (0.54), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 150 
 HIS   0.002   0.000   HIS A 197 
 PHE   0.014   0.001   PHE A  57 
 TYR   0.011   0.001   TYR F  25 
 ARG   0.012   0.001   ARG E 113 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 160
  time to evaluate  : 0.930 
Fit side-chains
REVERT: A   54 ASP cc_start: 0.8674 (t0) cc_final: 0.8400 (t0)
REVERT: A   59 LYS cc_start: 0.9102 (tmmt) cc_final: 0.8890 (tmtt)
REVERT: A  154 ASN cc_start: 0.9157 (t0) cc_final: 0.8683 (m-40)
REVERT: A  208 ASP cc_start: 0.8864 (t0) cc_final: 0.8453 (t0)
REVERT: E   96 LYS cc_start: 0.9315 (mmmt) cc_final: 0.9060 (mtmm)
REVERT: E  208 ASP cc_start: 0.8526 (t0) cc_final: 0.8239 (t0)
REVERT: D   13 ASP cc_start: 0.9484 (m-30) cc_final: 0.8870 (t0)
REVERT: D   54 ASP cc_start: 0.9126 (t0) cc_final: 0.8922 (t0)
REVERT: D   59 LYS cc_start: 0.9248 (tppt) cc_final: 0.8882 (ttpp)
REVERT: D   60 MET cc_start: 0.9458 (tpp) cc_final: 0.9040 (tpp)
REVERT: D   96 LYS cc_start: 0.9579 (tppp) cc_final: 0.9284 (tptp)
REVERT: D  100 ARG cc_start: 0.8773 (mmp80) cc_final: 0.8339 (mmp80)
REVERT: D  113 ARG cc_start: 0.8491 (mmp80) cc_final: 0.8242 (mmp80)
REVERT: D  208 ASP cc_start: 0.8820 (t0) cc_final: 0.8443 (t0)
REVERT: C   16 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8913 (mt)
REVERT: C   35 PHE cc_start: 0.8514 (t80) cc_final: 0.8271 (t80)
REVERT: C   59 LYS cc_start: 0.9367 (pptt) cc_final: 0.9071 (pptt)
REVERT: C   73 ASN cc_start: 0.9528 (m110) cc_final: 0.9260 (p0)
REVERT: C  116 ARG cc_start: 0.8845 (ttp80) cc_final: 0.8391 (ttp-110)
REVERT: C  142 TYR cc_start: 0.7000 (m-80) cc_final: 0.6379 (m-80)
REVERT: B   42 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8454 (ttpt)
REVERT: B  112 GLU cc_start: 0.8736 (tt0) cc_final: 0.8492 (tt0)
REVERT: B  122 ASP cc_start: 0.8905 (t0) cc_final: 0.8443 (t0)
REVERT: B  208 ASP cc_start: 0.8730 (t0) cc_final: 0.8396 (t0)
REVERT: F    8 ARG cc_start: 0.7062 (tmm-80) cc_final: 0.6838 (tmm-80)
REVERT: F   13 LYS cc_start: 0.8612 (pttp) cc_final: 0.8015 (pptt)
REVERT: G   42 MET cc_start: 0.8874 (mtp) cc_final: 0.8368 (ttm)
  outliers start: 18
  outliers final: 14
  residues processed: 173
  average time/residue: 0.2898
  time to fit residues: 63.7915
Evaluate side-chains
  170 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain C residue   10 HIS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  163 ASP
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain G residue   43 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 43 optimal weight:    5.9990
   chunk 93 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 103 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 0 optimal weight:    9.9990
   chunk 90 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** C 106 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 = 0.3270 r_free = 0.3270 target = 0.070026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.051619 restraints weight = 37370.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 4.25
r_work: 0.2657 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2680
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2680 r_free = 0.2680    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2680 r_free = 0.2680    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2680
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9270  Z= 0.242
  Angle     :  0.589   7.395  12551  Z= 0.294
  Chirality :  0.036   0.141   1470
  Planarity :  0.004   0.060   1567
  Dihedral  :  3.288  18.266   1248
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.55 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 17.27 %
    Favored  : 81.06 %
  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:  3.91 (0.25), residues: 1162
  helix:  3.02 (0.16), residues: 1032
  sheet:  None (None), residues: 0
  loop : -1.49 (0.55), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 150 
 HIS   0.002   0.000   HIS A 197 
 PHE   0.014   0.001   PHE A  57 
 TYR   0.011   0.001   TYR F  25 
 ARG   0.012   0.001   ARG E 113 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 162
  time to evaluate  : 1.123 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.9123 (tmmt) cc_final: 0.8916 (tmtt)
REVERT: A  208 ASP cc_start: 0.9085 (t0) cc_final: 0.8728 (t0)
REVERT: E   96 LYS cc_start: 0.9333 (mmmt) cc_final: 0.9040 (mtmm)
REVERT: E  208 ASP cc_start: 0.8739 (t0) cc_final: 0.8479 (t0)
REVERT: D   13 ASP cc_start: 0.9510 (m-30) cc_final: 0.8901 (t0)
REVERT: D   60 MET cc_start: 0.9493 (tpp) cc_final: 0.9125 (tpp)
REVERT: D   96 LYS cc_start: 0.9535 (tppp) cc_final: 0.9187 (tptp)
REVERT: D  113 ARG cc_start: 0.8510 (mmp80) cc_final: 0.8263 (mmp80)
REVERT: D  208 ASP cc_start: 0.8892 (t0) cc_final: 0.8571 (t0)
REVERT: C   16 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.8980 (mt)
REVERT: C   35 PHE cc_start: 0.8600 (t80) cc_final: 0.8361 (t80)
REVERT: C   73 ASN cc_start: 0.9477 (m110) cc_final: 0.9247 (p0)
REVERT: C  116 ARG cc_start: 0.9038 (ttp80) cc_final: 0.8640 (ttp-110)
REVERT: C  142 TYR cc_start: 0.7245 (m-80) cc_final: 0.6677 (m-80)
REVERT: B   42 LYS cc_start: 0.8950 (ttpt) cc_final: 0.8666 (ttpt)
REVERT: B  112 GLU cc_start: 0.9121 (tt0) cc_final: 0.8886 (tt0)
REVERT: B  116 ARG cc_start: 0.8850 (ttm-80) cc_final: 0.8348 (ttm-80)
REVERT: B  122 ASP cc_start: 0.9009 (t0) cc_final: 0.8600 (t0)
REVERT: B  208 ASP cc_start: 0.8921 (t0) cc_final: 0.8617 (t0)
REVERT: F   13 LYS cc_start: 0.8705 (pttp) cc_final: 0.8136 (pptt)
REVERT: G   42 MET cc_start: 0.9003 (mtp) cc_final: 0.8505 (ttm)
  outliers start: 16
  outliers final: 15
  residues processed: 175
  average time/residue: 0.3061
  time to fit residues: 68.6627
Evaluate side-chains
  173 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 157
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain C residue   10 HIS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  163 ASP
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain G residue   43 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0770
   chunk 34 optimal weight:    0.6980
   chunk 92 optimal weight:    0.3980
   chunk 104 optimal weight:    0.6980
   chunk 83 optimal weight:    0.7980
   chunk 112 optimal weight:    0.6980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
E  72 ASN
** C 106 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 = 0.3320 r_free = 0.3320 target = 0.071649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.052943 restraints weight = 53213.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.2882 rms_B_bonded: 4.97
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2883
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2883
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9270  Z= 0.202
  Angle     :  0.595   8.522  12551  Z= 0.299
  Chirality :  0.036   0.148   1470
  Planarity :  0.004   0.061   1567
  Dihedral  :  3.288  17.605   1248
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.64 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 17.79 %
    Favored  : 80.65 %
  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:  3.98 (0.25), residues: 1162
  helix:  3.11 (0.16), residues: 1022
  sheet:  None (None), residues: 0
  loop : -1.46 (0.53), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 150 
 HIS   0.002   0.000   HIS A 197 
 PHE   0.020   0.001   PHE D  87 
 TYR   0.009   0.001   TYR F  25 
 ARG   0.014   0.001   ARG E 113 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 163
  time to evaluate  : 1.295 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.9064 (tmmt) cc_final: 0.8588 (tppt)
REVERT: A  208 ASP cc_start: 0.8853 (t0) cc_final: 0.8456 (t0)
REVERT: E   26 MET cc_start: 0.8633 (mtm) cc_final: 0.8362 (mpp)
REVERT: E   96 LYS cc_start: 0.9293 (mmmt) cc_final: 0.9040 (mtmm)
REVERT: E  208 ASP cc_start: 0.8441 (t0) cc_final: 0.8157 (t0)
REVERT: D   13 ASP cc_start: 0.9480 (m-30) cc_final: 0.8895 (t0)
REVERT: D   42 LYS cc_start: 0.8911 (tmmt) cc_final: 0.8595 (ttpt)
REVERT: D   59 LYS cc_start: 0.9230 (tppt) cc_final: 0.8868 (ttpp)
REVERT: D   60 MET cc_start: 0.9419 (tpp) cc_final: 0.9006 (tpp)
REVERT: D   88 TYR cc_start: 0.8618 (t80) cc_final: 0.8382 (t80)
REVERT: D   96 LYS cc_start: 0.9564 (tppp) cc_final: 0.9273 (tptp)
REVERT: D  100 ARG cc_start: 0.8729 (mmp80) cc_final: 0.8266 (mmp80)
REVERT: D  113 ARG cc_start: 0.8520 (mmp80) cc_final: 0.8256 (mmp80)
REVERT: D  153 MET cc_start: 0.8464 (mmm) cc_final: 0.8078 (tpp)
REVERT: D  201 LYS cc_start: 0.8133 (mtpt) cc_final: 0.7829 (ttmm)
REVERT: D  208 ASP cc_start: 0.8803 (t0) cc_final: 0.8437 (t0)
REVERT: C   16 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8927 (mt)
REVERT: C   35 PHE cc_start: 0.8482 (t80) cc_final: 0.8226 (t80)
REVERT: C   73 ASN cc_start: 0.9491 (m110) cc_final: 0.9275 (p0)
REVERT: C  116 ARG cc_start: 0.8851 (ttp80) cc_final: 0.8414 (ttp-110)
REVERT: C  142 TYR cc_start: 0.6967 (m-80) cc_final: 0.6396 (m-80)
REVERT: B   42 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8497 (ttpt)
REVERT: B   60 MET cc_start: 0.9112 (ttp) cc_final: 0.8793 (tpp)
REVERT: B  116 ARG cc_start: 0.8561 (ttm-80) cc_final: 0.7921 (ttm-80)
REVERT: B  208 ASP cc_start: 0.8666 (t0) cc_final: 0.8369 (t0)
REVERT: F   13 LYS cc_start: 0.8610 (pttp) cc_final: 0.8011 (pptt)
REVERT: G   42 MET cc_start: 0.8787 (mtp) cc_final: 0.8279 (ttm)
  outliers start: 15
  outliers final: 13
  residues processed: 175
  average time/residue: 0.3732
  time to fit residues: 83.1475
Evaluate side-chains
  171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 157
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain C residue   10 HIS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain G residue   43 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 94 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   chunk 74 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 64 optimal weight:   10.0000
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
E  72 ASN
** C 106 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 = 0.3307 r_free = 0.3307 target = 0.071360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.052794 restraints weight = 38055.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 4.22
r_work: 0.2711 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2719
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2719
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.2606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9270  Z= 0.223
  Angle     :  0.613   8.883  12551  Z= 0.307
  Chirality :  0.036   0.162   1470
  Planarity :  0.004   0.065   1567
  Dihedral  :  3.246  17.085   1248
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.73 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 18.11 %
    Favored  : 80.54 %
  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:  3.91 (0.25), residues: 1162
  helix:  3.03 (0.16), residues: 1031
  sheet:  None (None), residues: 0
  loop : -1.54 (0.55), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 150 
 HIS   0.002   0.001   HIS D 197 
 PHE   0.018   0.001   PHE D  87 
 TYR   0.017   0.001   TYR B  38 
 ARG   0.013   0.001   ARG E 113 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4259.82 seconds
wall clock time: 75 minutes 39.47 seconds (4539.47 seconds total)