Starting phenix.real_space_refine
on Thu Feb 13 14:23:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vlw_43346/02_2025/8vlw_43346.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vlw_43346/02_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_43346/02_2025/8vlw_43346.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vlw_43346/02_2025/8vlw_43346.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vlw_43346/02_2025/8vlw_43346.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vlw_43346/02_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-5592/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: 6.53, per 1000 atoms: 0.72
  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: 2.30
  Conformation dependent library (CDL) restraints added in 1.4 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: 0.73
  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: 2.40

  Time building geometry restraints manager: 2.63 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:             5.630
  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:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.780
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.300
-------------------------------------------------------------------------------
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  : 0.913 
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: 0.2931
  time to fit residues: 81.8155
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  : 1.110 
-------------------------------------------------------------------------------
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 = 0.3317 r_free = 0.3317 target = 0.071496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.053031 restraints weight = 55662.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 4.96
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2875
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2875 r_free = 0.2875    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 = 0.2875 r_free = 0.2875    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2875
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
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   7.396  12551  Z= 0.317
  Chirality :  0.038   0.162   1470
  Planarity :  0.005   0.054   1567
  Dihedral  :  3.793  27.660   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  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.8644 (t0) cc_final: 0.8385 (t0)
REVERT: A  208 ASP cc_start: 0.8833 (t0) cc_final: 0.8446 (t0)
REVERT: E   26 MET cc_start: 0.8569 (mtm) cc_final: 0.8041 (mtm)
REVERT: E   54 ASP cc_start: 0.8642 (t70) cc_final: 0.8410 (t0)
REVERT: E  208 ASP cc_start: 0.8321 (t0) cc_final: 0.8070 (t0)
REVERT: D   60 MET cc_start: 0.9474 (tpp) cc_final: 0.9064 (tpp)
REVERT: D  154 ASN cc_start: 0.8977 (t0) cc_final: 0.8583 (t0)
REVERT: D  197 HIS cc_start: 0.8427 (t-90) cc_final: 0.8203 (t-170)
REVERT: D  208 ASP cc_start: 0.8571 (t0) cc_final: 0.8329 (t0)
REVERT: C   59 LYS cc_start: 0.9367 (pptt) cc_final: 0.9103 (pptt)
REVERT: C   88 TYR cc_start: 0.8238 (t80) cc_final: 0.7735 (t80)
REVERT: C   99 LYS cc_start: 0.9462 (tppt) cc_final: 0.8904 (mmtm)
REVERT: C  116 ARG cc_start: 0.8736 (ttp80) cc_final: 0.8326 (ttp-110)
REVERT: C  142 TYR cc_start: 0.6892 (m-80) cc_final: 0.6394 (m-80)
REVERT: B   42 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8461 (tttt)
REVERT: B   54 ASP cc_start: 0.8535 (t0) cc_final: 0.8273 (t0)
REVERT: B  109 GLU cc_start: 0.8464 (tt0) cc_final: 0.8253 (tt0)
REVERT: B  208 ASP cc_start: 0.8611 (t0) cc_final: 0.8240 (t0)
  outliers start: 9
  outliers final: 8
  residues processed: 185
  average time/residue: 0.3173
  time to fit residues: 73.8730
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  : 1.052 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 16 optimal weight:    0.0040
   chunk 20 optimal weight:    0.7980
   chunk 112 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9980
   chunk 106 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.5392

-------------------------------------------------------------------------------
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 = 0.3285 r_free = 0.3285 target = 0.070764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.051791 restraints weight = 56137.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 5.17
r_work (final): 0.2839
-------------------------------------------------------------------------------
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 = 0.31   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 = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1749

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= 0.199
  Angle     :  0.575   7.368  12551  Z= 0.287
  Chirality :  0.036   0.154   1470
  Planarity :  0.004   0.047   1567
  Dihedral  :  3.579  26.385   1248
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  1.90 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 11.97 %
    Favored  : 86.78 %
  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:  3.45 (0.25), residues: 1162
  helix:  2.77 (0.16), residues: 1024
  sheet:  None (None), residues: 0
  loop : -1.86 (0.51), residues: 138

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   0.018   0.001   PHE D 212 
 TYR   0.010   0.001   TYR D 128 
 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
  188 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 176
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.8633 (t0) cc_final: 0.8401 (t0)
REVERT: A  154 ASN cc_start: 0.9116 (t0) cc_final: 0.8695 (m-40)
REVERT: A  208 ASP cc_start: 0.8835 (t0) cc_final: 0.8433 (t0)
REVERT: E   49 LYS cc_start: 0.9187 (tptp) cc_final: 0.8904 (tppt)
REVERT: E   96 LYS cc_start: 0.9411 (mmmt) cc_final: 0.9121 (mtmm)
REVERT: E  208 ASP cc_start: 0.8427 (t0) cc_final: 0.8124 (t0)
REVERT: D   59 LYS cc_start: 0.9119 (mmmt) cc_final: 0.8861 (ttpp)
REVERT: D   60 MET cc_start: 0.9500 (tpp) cc_final: 0.9067 (tpp)
REVERT: D   96 LYS cc_start: 0.9664 (tppp) cc_final: 0.9314 (tptp)
REVERT: D  154 ASN cc_start: 0.8936 (t0) cc_final: 0.8620 (t0)
REVERT: D  208 ASP cc_start: 0.8683 (t0) cc_final: 0.8329 (t0)
REVERT: C   59 LYS cc_start: 0.9374 (pptt) cc_final: 0.9098 (pptt)
REVERT: C   88 TYR cc_start: 0.8263 (t80) cc_final: 0.7709 (t80)
REVERT: C   91 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8442 (tt)
REVERT: C   99 LYS cc_start: 0.9484 (tppt) cc_final: 0.8989 (mmtm)
REVERT: C  116 ARG cc_start: 0.8756 (ttp80) cc_final: 0.8319 (ttp-110)
REVERT: C  142 TYR cc_start: 0.6906 (m-80) cc_final: 0.6385 (m-80)
REVERT: B   42 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8410 (ttpt)
REVERT: B   93 GLU cc_start: 0.9226 (tp30) cc_final: 0.8969 (tp30)
REVERT: B  109 GLU cc_start: 0.8468 (tt0) cc_final: 0.8226 (tt0)
REVERT: B  122 ASP cc_start: 0.8872 (t0) cc_final: 0.8444 (t0)
REVERT: B  208 ASP cc_start: 0.8658 (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: 0.8790 (mtp) cc_final: 0.8318 (ttm)
  outliers start: 12
  outliers final: 5
  residues processed: 186
  average time/residue: 0.2964
  time to fit residues: 70.3416
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  : 1.048 
-------------------------------------------------------------------------------
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  163 ASP
Chi-restraints excluded: chain C residue  211 LEU
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:    2.9990
   chunk 78 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 102 optimal weight:    0.7980
   chunk 86 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3270 r_free = 0.3270 target = 0.070006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.051638 restraints weight = 42752.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.2841 rms_B_bonded: 4.51
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2843
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    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 = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2843
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.1971

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= 0.226
  Angle     :  0.568   6.965  12551  Z= 0.286
  Chirality :  0.036   0.153   1470
  Planarity :  0.004   0.047   1567
  Dihedral  :  3.429  23.202   1248
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.73 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 14.26 %
    Favored  : 83.66 %
  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:  3.68 (0.25), residues: 1162
  helix:  2.91 (0.16), residues: 1025
  sheet:  None (None), residues: 0
  loop : -1.72 (0.52), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 150 
 HIS   0.003   0.001   HIS E  56 
 PHE   0.016   0.001   PHE D 212 
 TYR   0.012   0.001   TYR A 142 
 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
  192 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 172
  time to evaluate  : 1.015 
Fit side-chains
REVERT: A   54 ASP cc_start: 0.8667 (t0) cc_final: 0.8454 (t0)
REVERT: A  154 ASN cc_start: 0.9105 (t0) cc_final: 0.8675 (m-40)
REVERT: A  208 ASP cc_start: 0.8864 (t0) cc_final: 0.8438 (t0)
REVERT: E   49 LYS cc_start: 0.9210 (tptp) cc_final: 0.8884 (tppt)
REVERT: E   96 LYS cc_start: 0.9377 (mmmt) cc_final: 0.9086 (mtmm)
REVERT: E  208 ASP cc_start: 0.8423 (t0) cc_final: 0.8160 (t0)
REVERT: D   13 ASP cc_start: 0.9522 (m-30) cc_final: 0.8852 (t0)
REVERT: D   59 LYS cc_start: 0.9120 (mmmt) cc_final: 0.8837 (ttpp)
REVERT: D   60 MET cc_start: 0.9482 (tpp) cc_final: 0.9015 (tpp)
REVERT: D   96 LYS cc_start: 0.9653 (tppp) cc_final: 0.9306 (tptp)
REVERT: D  154 ASN cc_start: 0.8960 (t0) cc_final: 0.8636 (t0)
REVERT: D  197 HIS cc_start: 0.8347 (t-90) cc_final: 0.8128 (t-170)
REVERT: D  208 ASP cc_start: 0.8724 (t0) cc_final: 0.8316 (t0)
REVERT: C   59 LYS cc_start: 0.9364 (pptt) cc_final: 0.9085 (pptt)
REVERT: C   99 LYS cc_start: 0.9485 (tppt) cc_final: 0.8939 (mmtm)
REVERT: C  116 ARG cc_start: 0.8766 (ttp80) cc_final: 0.8317 (ttp-110)
REVERT: C  142 TYR cc_start: 0.6955 (m-80) cc_final: 0.6377 (m-80)
REVERT: B   42 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8421 (ttpt)
REVERT: B  122 ASP cc_start: 0.8891 (t0) cc_final: 0.8451 (t0)
REVERT: B  208 ASP cc_start: 0.8662 (t0) cc_final: 0.8306 (t0)
REVERT: F   13 LYS cc_start: 0.8604 (pttp) cc_final: 0.8012 (pptt)
REVERT: G   42 MET cc_start: 0.8831 (mtp) cc_final: 0.8310 (ttm)
  outliers start: 20
  outliers final: 11
  residues processed: 184
  average time/residue: 0.3217
  time to fit residues: 74.4847
Evaluate side-chains
  177 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 166
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain E residue  130 LEU
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain D residue  217 ILE
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:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9990
   chunk 88 optimal weight:    0.8980
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3271 r_free = 0.3271 target = 0.070088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.050993 restraints weight = 46497.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.2818 rms_B_bonded: 4.77
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2816
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2816 r_free = 0.2816    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2816 r_free = 0.2816    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2816
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.2104

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= 0.241
  Angle     :  0.573   7.529  12551  Z= 0.287
  Chirality :  0.036   0.145   1470
  Planarity :  0.004   0.046   1567
  Dihedral  :  3.374  22.220   1248
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.64 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 14.36 %
    Favored  : 83.45 %
  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:  3.79 (0.25), residues: 1162
  helix:  2.98 (0.16), residues: 1026
  sheet:  None (None), residues: 0
  loop : -1.67 (0.52), residues: 136

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   0.012   0.001   TYR A 142 
 ARG   0.010   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
  192 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 1.077 
Fit side-chains
REVERT: A   26 MET cc_start: 0.8848 (mtm) cc_final: 0.8591 (mpp)
REVERT: A   54 ASP cc_start: 0.8682 (t0) cc_final: 0.8479 (t0)
REVERT: A  208 ASP cc_start: 0.8881 (t0) cc_final: 0.8460 (t0)
REVERT: E   26 MET cc_start: 0.8571 (mtm) cc_final: 0.7893 (mtm)
REVERT: E   49 LYS cc_start: 0.9198 (tptp) cc_final: 0.8859 (tppt)
REVERT: E   96 LYS cc_start: 0.9375 (mmmt) cc_final: 0.9108 (mtmm)
REVERT: E  208 ASP cc_start: 0.8520 (t0) cc_final: 0.8225 (t0)
REVERT: D   13 ASP cc_start: 0.9506 (m-30) cc_final: 0.8872 (t0)
REVERT: D   59 LYS cc_start: 0.9163 (mmmt) cc_final: 0.8861 (ttpp)
REVERT: D   60 MET cc_start: 0.9473 (tpp) cc_final: 0.8998 (tpp)
REVERT: D   96 LYS cc_start: 0.9638 (tppp) cc_final: 0.9297 (tptp)
REVERT: D  197 HIS cc_start: 0.8478 (t-90) cc_final: 0.8268 (t-170)
REVERT: D  208 ASP cc_start: 0.8767 (t0) cc_final: 0.8355 (t0)
REVERT: C   59 LYS cc_start: 0.9384 (pptt) cc_final: 0.9097 (pptt)
REVERT: C   99 LYS cc_start: 0.9489 (tppt) cc_final: 0.8939 (mmtm)
REVERT: C  116 ARG cc_start: 0.8780 (ttp80) cc_final: 0.8356 (ttp-110)
REVERT: C  142 TYR cc_start: 0.7017 (m-80) cc_final: 0.6388 (m-80)
REVERT: B   42 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8442 (ttpt)
REVERT: B  122 ASP cc_start: 0.8940 (t0) cc_final: 0.8499 (t0)
REVERT: B  208 ASP cc_start: 0.8705 (t0) cc_final: 0.8343 (t0)
REVERT: F   13 LYS cc_start: 0.8619 (pttp) cc_final: 0.8050 (pptt)
REVERT: G   42 MET cc_start: 0.8881 (mtp) cc_final: 0.8343 (ttm)
  outliers start: 21
  outliers final: 13
  residues processed: 185
  average time/residue: 0.3031
  time to fit residues: 71.3953
Evaluate side-chains
  173 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 160
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain E residue  130 LEU
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain D residue  217 ILE
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  181 THR
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:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9980
   chunk 95 optimal weight:    0.4980
   chunk 89 optimal weight:    0.8980
   chunk 81 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3278 r_free = 0.3278 target = 0.070476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.051448 restraints weight = 47119.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.2829 rms_B_bonded: 4.77
r_work (final): 0.2829
-------------------------------------------------------------------------------
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: 0.8491
moved from start:          0.2234

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= 0.213
  Angle     :  0.558   6.628  12551  Z= 0.281
  Chirality :  0.036   0.155   1470
  Planarity :  0.004   0.047   1567
  Dihedral  :  3.338  21.382   1248
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.81 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.61 %
    Favored  : 82.21 %
  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:  3.93 (0.25), residues: 1162
  helix:  3.07 (0.16), residues: 1025
  sheet:  None (None), residues: 0
  loop : -1.60 (0.52), 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   0.014   0.001   PHE D 212 
 TYR   0.014   0.001   TYR C  71 
 ARG   0.010   0.001   ARG E 113 

*********************** 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
  189 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 168
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
REVERT: A  208 ASP cc_start: 0.8888 (t0) cc_final: 0.8459 (t0)
REVERT: E   49 LYS cc_start: 0.9205 (tptp) cc_final: 0.8856 (tppt)
REVERT: E  208 ASP cc_start: 0.8521 (t0) cc_final: 0.8216 (t0)
REVERT: D   13 ASP cc_start: 0.9492 (m-30) cc_final: 0.8865 (t0)
REVERT: D   60 MET cc_start: 0.9449 (tpp) cc_final: 0.9034 (tpp)
REVERT: D   96 LYS cc_start: 0.9630 (tppp) cc_final: 0.9298 (tptp)
REVERT: D  208 ASP cc_start: 0.8785 (t0) cc_final: 0.8417 (t0)
REVERT: C   16 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8871 (mt)
REVERT: C   59 LYS cc_start: 0.9351 (pptt) cc_final: 0.9057 (pptt)
REVERT: C   99 LYS cc_start: 0.9495 (tppt) cc_final: 0.8954 (mmtm)
REVERT: C  116 ARG cc_start: 0.8770 (ttp80) cc_final: 0.8353 (ttp-110)
REVERT: C  142 TYR cc_start: 0.7054 (m-80) cc_final: 0.6428 (m-80)
REVERT: B   42 LYS cc_start: 0.8764 (ttpt) cc_final: 0.8453 (ttpt)
REVERT: B  122 ASP cc_start: 0.8890 (t0) cc_final: 0.8445 (t0)
REVERT: B  208 ASP cc_start: 0.8706 (t0) cc_final: 0.8360 (t0)
REVERT: F   13 LYS cc_start: 0.8618 (pttp) cc_final: 0.8046 (pptt)
  outliers start: 21
  outliers final: 12
  residues processed: 183
  average time/residue: 0.3023
  time to fit residues: 70.3836
Evaluate side-chains
  174 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 161
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
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  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:    0.8980
   chunk 23 optimal weight:    0.1980
   chunk 4 optimal weight:    0.6980
   chunk 22 optimal weight:    8.9990
   chunk 7 optimal weight:    0.0370
   chunk 43 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9990
   chunk 70 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.4458

-------------------------------------------------------------------------------
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 = 0.3288 r_free = 0.3288 target = 0.070924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.052214 restraints weight = 47964.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 4.85
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2853
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2853
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.2351

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= 0.191
  Angle     :  0.569   8.881  12551  Z= 0.283
  Chirality :  0.035   0.153   1470
  Planarity :  0.004   0.051   1567
  Dihedral  :  3.295  20.358   1248
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.47 %
    Favored  : 98.45 %
  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:  4.03 (0.25), residues: 1162
  helix:  3.12 (0.16), residues: 1026
  sheet:  None (None), residues: 0
  loop : -1.51 (0.53), residues: 136

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   0.012   0.001   PHE A  57 
 TYR   0.011   0.001   TYR C  71 
 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
  185 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 169
  time to evaluate  : 0.994 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.9043 (tmmt) cc_final: 0.8578 (tppt)
REVERT: A  154 ASN cc_start: 0.8999 (t0) cc_final: 0.8635 (m-40)
REVERT: A  208 ASP cc_start: 0.8828 (t0) cc_final: 0.8432 (t0)
REVERT: E   26 MET cc_start: 0.8574 (mtm) cc_final: 0.8155 (mtm)
REVERT: E   49 LYS cc_start: 0.9207 (tptp) cc_final: 0.8853 (tppt)
REVERT: E   96 LYS cc_start: 0.9323 (mmmt) cc_final: 0.9067 (mtmm)
REVERT: E  208 ASP cc_start: 0.8420 (t0) cc_final: 0.8147 (t0)
REVERT: D   13 ASP cc_start: 0.9487 (m-30) cc_final: 0.8871 (t0)
REVERT: D   54 ASP cc_start: 0.9132 (t0) cc_final: 0.8925 (t0)
REVERT: D   59 LYS cc_start: 0.9220 (tppt) cc_final: 0.8881 (ttpp)
REVERT: D   60 MET cc_start: 0.9454 (tpp) cc_final: 0.9024 (tpp)
REVERT: D   96 LYS cc_start: 0.9610 (tppp) cc_final: 0.9280 (tptp)
REVERT: D  208 ASP cc_start: 0.8761 (t0) cc_final: 0.8398 (t0)
REVERT: C   16 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8910 (mt)
REVERT: C   35 PHE cc_start: 0.8414 (t80) cc_final: 0.8157 (t80)
REVERT: C   59 LYS cc_start: 0.9346 (pptt) cc_final: 0.9054 (pptt)
REVERT: C   99 LYS cc_start: 0.9495 (tppt) cc_final: 0.8944 (mmtm)
REVERT: C  116 ARG cc_start: 0.8741 (ttp80) cc_final: 0.8476 (ttp80)
REVERT: C  142 TYR cc_start: 0.6967 (m-80) cc_final: 0.6350 (m-80)
REVERT: B   42 LYS cc_start: 0.8733 (ttpt) cc_final: 0.8429 (ttpt)
REVERT: B   60 MET cc_start: 0.9113 (ttp) cc_final: 0.8771 (tpp)
REVERT: B  122 ASP cc_start: 0.8815 (t0) cc_final: 0.8351 (t0)
REVERT: B  208 ASP cc_start: 0.8687 (t0) cc_final: 0.8347 (t0)
REVERT: F   13 LYS cc_start: 0.8593 (pttp) cc_final: 0.8001 (pptt)
REVERT: G   42 MET cc_start: 0.8784 (mtp) cc_final: 0.8245 (ttm)
  outliers start: 16
  outliers final: 14
  residues processed: 180
  average time/residue: 0.3002
  time to fit residues: 68.9445
Evaluate side-chains
  175 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 160
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
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   45 MET
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:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3275 r_free = 0.3275 target = 0.070343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.050772 restraints weight = 63541.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 5.46
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2813
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2812
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.2415

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= 0.232
  Angle     :  0.580   7.838  12551  Z= 0.289
  Chirality :  0.036   0.147   1470
  Planarity :  0.004   0.057   1567
  Dihedral  :  3.248  19.394   1248
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.55 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 17.48 %
    Favored  : 80.85 %
  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:  4.01 (0.25), residues: 1162
  helix:  3.11 (0.16), residues: 1025
  sheet:  None (None), residues: 0
  loop : -1.47 (0.54), residues: 137

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   0.017   0.001   TYR B  38 
 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: 16
    poor density    : 162
  time to evaluate  : 1.018 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.9080 (tmmt) cc_final: 0.8620 (tppt)
REVERT: A  208 ASP cc_start: 0.8850 (t0) cc_final: 0.8455 (t0)
REVERT: E   26 MET cc_start: 0.8606 (mtm) cc_final: 0.8041 (mtm)
REVERT: E   96 LYS cc_start: 0.9308 (mmmt) cc_final: 0.9049 (mtmm)
REVERT: E  208 ASP cc_start: 0.8505 (t0) cc_final: 0.8225 (t0)
REVERT: D   13 ASP cc_start: 0.9487 (m-30) cc_final: 0.8870 (t0)
REVERT: D   59 LYS cc_start: 0.9240 (tppt) cc_final: 0.8874 (ttpp)
REVERT: D   60 MET cc_start: 0.9461 (tpp) cc_final: 0.9029 (tpp)
REVERT: D   96 LYS cc_start: 0.9604 (tppp) cc_final: 0.9279 (tptp)
REVERT: D  100 ARG cc_start: 0.8738 (mmp80) cc_final: 0.8283 (mmp80)
REVERT: D  208 ASP cc_start: 0.8836 (t0) cc_final: 0.8457 (t0)
REVERT: C   16 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8908 (mt)
REVERT: C   35 PHE cc_start: 0.8484 (t80) cc_final: 0.8236 (t80)
REVERT: C   59 LYS cc_start: 0.9369 (pptt) cc_final: 0.9070 (pptt)
REVERT: C   73 ASN cc_start: 0.9529 (m110) cc_final: 0.9262 (p0)
REVERT: C   99 LYS cc_start: 0.9498 (tppt) cc_final: 0.8934 (mmtm)
REVERT: C  116 ARG cc_start: 0.8753 (ttp80) cc_final: 0.8359 (ttp-110)
REVERT: C  142 TYR cc_start: 0.7021 (m-80) cc_final: 0.6398 (m-80)
REVERT: B   42 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8431 (ttpt)
REVERT: B   60 MET cc_start: 0.9115 (ttp) cc_final: 0.8775 (tpp)
REVERT: B  122 ASP cc_start: 0.8871 (t0) cc_final: 0.8407 (t0)
REVERT: B  208 ASP cc_start: 0.8713 (t0) cc_final: 0.8375 (t0)
REVERT: F   13 LYS cc_start: 0.8607 (pttp) cc_final: 0.8012 (pptt)
REVERT: G   42 MET cc_start: 0.8844 (mtp) cc_final: 0.8269 (ttm)
  outliers start: 16
  outliers final: 13
  residues processed: 174
  average time/residue: 0.2996
  time to fit residues: 66.5061
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  : 1.010 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 93 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9990
   chunk 103 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0870
   chunk 32 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 90 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 59 optimal weight:    0.0270
   overall best weight:    0.4416

-------------------------------------------------------------------------------
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 = 0.3296 r_free = 0.3296 target = 0.071492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.053062 restraints weight = 37058.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 4.23
r_work: 0.2694 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2715
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2715 r_free = 0.2715    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 = 0.2715 r_free = 0.2715    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2715
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.2510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9270  Z= 0.193
  Angle     :  0.570   7.571  12551  Z= 0.286
  Chirality :  0.035   0.148   1470
  Planarity :  0.004   0.057   1567
  Dihedral  :  3.242  18.134   1248
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.29 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 17.90 %
    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:  4.10 (0.25), residues: 1162
  helix:  3.17 (0.16), residues: 1026
  sheet:  None (None), residues: 0
  loop : -1.46 (0.53), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 150 
 HIS   0.002   0.000   HIS B  56 
 PHE   0.012   0.001   PHE A  57 
 TYR   0.016   0.001   TYR B  38 
 ARG   0.013   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
  184 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 169
  time to evaluate  : 1.046 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.9087 (tmmt) cc_final: 0.8645 (tppt)
REVERT: A  154 ASN cc_start: 0.9125 (t0) cc_final: 0.8697 (m-40)
REVERT: A  208 ASP cc_start: 0.9071 (t0) cc_final: 0.8724 (t0)
REVERT: E   26 MET cc_start: 0.8982 (mtm) cc_final: 0.8479 (mtm)
REVERT: E   96 LYS cc_start: 0.9311 (mmmt) cc_final: 0.9028 (mtmm)
REVERT: E  208 ASP cc_start: 0.8694 (t0) cc_final: 0.8450 (t0)
REVERT: D   13 ASP cc_start: 0.9501 (m-30) cc_final: 0.8922 (t0)
REVERT: D   60 MET cc_start: 0.9477 (tpp) cc_final: 0.9092 (tpp)
REVERT: D   96 LYS cc_start: 0.9560 (tppp) cc_final: 0.9199 (tptp)
REVERT: D  100 ARG cc_start: 0.8810 (mmp80) cc_final: 0.8337 (mmp80)
REVERT: D  208 ASP cc_start: 0.8827 (t0) cc_final: 0.8542 (t0)
REVERT: C   16 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.8988 (mt)
REVERT: C   35 PHE cc_start: 0.8549 (t80) cc_final: 0.8294 (t80)
REVERT: C   73 ASN cc_start: 0.9465 (m110) cc_final: 0.9244 (p0)
REVERT: C  116 ARG cc_start: 0.8959 (ttp80) cc_final: 0.8755 (ttp80)
REVERT: C  142 TYR cc_start: 0.7176 (m-80) cc_final: 0.6583 (m-80)
REVERT: B   42 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8657 (ttpt)
REVERT: B   60 MET cc_start: 0.9341 (ttp) cc_final: 0.8928 (tpp)
REVERT: B  208 ASP cc_start: 0.8863 (t0) cc_final: 0.8567 (t0)
REVERT: F   13 LYS cc_start: 0.8680 (pttp) cc_final: 0.8121 (pptt)
REVERT: G   42 MET cc_start: 0.8967 (mtp) cc_final: 0.8447 (ttm)
  outliers start: 15
  outliers final: 13
  residues processed: 181
  average time/residue: 0.2903
  time to fit residues: 67.2914
Evaluate side-chains
  175 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 161
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 92 optimal weight:    2.9990
   chunk 104 optimal weight:    0.5980
   chunk 83 optimal weight:    0.7980
   chunk 112 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3301 r_free = 0.3301 target = 0.071150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.051776 restraints weight = 54550.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 5.06
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2863
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2863
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9270  Z= 0.227
  Angle     :  0.599   7.552  12551  Z= 0.301
  Chirality :  0.036   0.158   1470
  Planarity :  0.004   0.063   1567
  Dihedral  :  3.199  17.466   1248
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.47 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 18.83 %
    Favored  : 79.81 %
  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:  4.05 (0.25), residues: 1162
  helix:  3.13 (0.16), residues: 1026
  sheet:  None (None), residues: 0
  loop : -1.37 (0.54), residues: 136

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   0.016   0.001   TYR B  38 
 ARG   0.013   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
  171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 158
  time to evaluate  : 0.972 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.9081 (tmmt) cc_final: 0.8632 (tppt)
REVERT: A  208 ASP cc_start: 0.8854 (t0) cc_final: 0.8472 (t0)
REVERT: E   26 MET cc_start: 0.8599 (mtm) cc_final: 0.7960 (mtm)
REVERT: E   54 ASP cc_start: 0.8783 (t0) cc_final: 0.8572 (t0)
REVERT: E   96 LYS cc_start: 0.9297 (mmmt) cc_final: 0.9087 (mtmm)
REVERT: E  208 ASP cc_start: 0.8530 (t0) cc_final: 0.8250 (t0)
REVERT: D   13 ASP cc_start: 0.9482 (m-30) cc_final: 0.8904 (t0)
REVERT: D   59 LYS cc_start: 0.9258 (tppt) cc_final: 0.8889 (ttpp)
REVERT: D   60 MET cc_start: 0.9431 (tpp) cc_final: 0.9015 (tpp)
REVERT: D   96 LYS cc_start: 0.9574 (tppp) cc_final: 0.9257 (tptp)
REVERT: D  100 ARG cc_start: 0.8780 (mmp80) cc_final: 0.8291 (mmp80)
REVERT: D  208 ASP cc_start: 0.8845 (t0) cc_final: 0.8489 (t0)
REVERT: C   16 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8951 (mt)
REVERT: C   35 PHE cc_start: 0.8502 (t80) cc_final: 0.8250 (t80)
REVERT: C   73 ASN cc_start: 0.9484 (m110) cc_final: 0.9274 (p0)
REVERT: C  116 ARG cc_start: 0.8759 (ttp80) cc_final: 0.8378 (ttp-110)
REVERT: C  142 TYR cc_start: 0.7006 (m-80) cc_final: 0.6389 (m-80)
REVERT: B   26 MET cc_start: 0.8562 (mtp) cc_final: 0.8336 (mtm)
REVERT: B   42 LYS cc_start: 0.8794 (ttpt) cc_final: 0.8484 (ttpt)
REVERT: B   60 MET cc_start: 0.9110 (ttp) cc_final: 0.8799 (tpp)
REVERT: B  208 ASP cc_start: 0.8706 (t0) cc_final: 0.8416 (t0)
REVERT: F   13 LYS cc_start: 0.8633 (pttp) cc_final: 0.8034 (pptt)
REVERT: G   42 MET cc_start: 0.8819 (mtp) cc_final: 0.8238 (ttm)
  outliers start: 13
  outliers final: 11
  residues processed: 168
  average time/residue: 0.3055
  time to fit residues: 65.1877
Evaluate side-chains
  168 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 156
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
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   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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 94 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 64 optimal weight:    6.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3304 r_free = 0.3304 target = 0.071172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.052722 restraints weight = 38217.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 4.23
r_work: 0.2693 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.2693
-------------------------------------------------------------------------------
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: 0.8572
moved from start:          0.2582

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= 0.236
  Angle     :  0.610   7.690  12551  Z= 0.305
  Chirality :  0.036   0.159   1470
  Planarity :  0.004   0.064   1567
  Dihedral  :  3.201  17.092   1248
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.64 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 18.73 %
    Favored  : 79.92 %
  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:  4.00 (0.25), residues: 1162
  helix:  3.10 (0.16), residues: 1027
  sheet:  None (None), residues: 0
  loop : -1.52 (0.54), residues: 135

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   0.027   0.001   PHE D 198 
 TYR   0.015   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: 3938.40 seconds
wall clock time: 71 minutes 17.82 seconds (4277.82 seconds total)