Starting phenix.real_space_refine
on Wed Sep 17 14:12:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vlw_43346/09_2025/8vlw_43346.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vlw_43346/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vlw_43346/09_2025/8vlw_43346.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vlw_43346/09_2025/8vlw_43346.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vlw_43346/09_2025/8vlw_43346.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vlw_43346/09_2025/8vlw_43346.map"
  }
  resolution = 3.34
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.44, per 1000 atoms: 0.27
  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: 0.83
  Conformation dependent library (CDL) restraints added in 401.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.23
  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: 1.42

  Time building geometry restraints manager: 1.09 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:             6.520
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.060
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.460
-------------------------------------------------------------------------------
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= 0.923
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.023   0.004   ARG A 222 
 TYR   0.047   0.009   TYR C 206 
 PHE   0.057   0.010   PHE C  35 
 TRP   0.040   0.009   TRP B 150 
 HIS   0.039   0.009   HIS E  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.01340 ( 9270)
  covalent geometry    : angle       1.22303 (12551)
  hydrogen bonds       : bond        0.10148 (  818)
  hydrogen bonds       : angle       4.58823 ( 2455)

*********************** 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  : 0.403 
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: 0.1373
  time to fit residues: 38.6448
Evaluate side-chains
  160 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.6980
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3312 r_free = 0.3312 target = 0.071243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.052680 restraints weight = 49190.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 4.70
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2868
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2868 r_free = 0.2868    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 = 0.2868 r_free = 0.2868    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2868
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9270  Z= 0.155
  Angle     :  0.634   7.435  12551  Z= 0.319
  Chirality :  0.038   0.165   1470
  Planarity :  0.005   0.053   1567
  Dihedral  :  3.791  27.601   1248
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  1.64 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 10.30 %
    Favored  : 88.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.93 (0.25), residues: 1162
  helix:  2.42 (0.16), residues: 1023
  sheet:  None (None), residues: 0
  loop : -1.99 (0.50), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 113 
 TYR   0.011   0.001   TYR B 206 
 PHE   0.023   0.002   PHE D 212 
 TRP   0.007   0.001   TRP B 150 
 HIS   0.004   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 9270)
  covalent geometry    : angle       0.63354 (12551)
  hydrogen bonds       : bond        0.04466 (  818)
  hydrogen bonds       : angle       3.57057 ( 2455)

*********************** 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: 10
    poor density    : 176
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.8665 (t0) cc_final: 0.8401 (t0)
REVERT: A  208 ASP cc_start: 0.8825 (t0) cc_final: 0.8432 (t0)
REVERT: E   26 MET cc_start: 0.8566 (mtm) cc_final: 0.8066 (mtm)
REVERT: E   54 ASP cc_start: 0.8636 (t70) cc_final: 0.8408 (t0)
REVERT: E  208 ASP cc_start: 0.8360 (t0) cc_final: 0.8102 (t0)
REVERT: D   26 MET cc_start: 0.8773 (mtp) cc_final: 0.8442 (mtm)
REVERT: D  154 ASN cc_start: 0.8982 (t0) cc_final: 0.8584 (t0)
REVERT: D  197 HIS cc_start: 0.8501 (t-90) cc_final: 0.8277 (t-170)
REVERT: D  208 ASP cc_start: 0.8582 (t0) cc_final: 0.8336 (t0)
REVERT: C   59 LYS cc_start: 0.9371 (pptt) cc_final: 0.9111 (pptt)
REVERT: C   88 TYR cc_start: 0.8294 (t80) cc_final: 0.7742 (t80)
REVERT: C   99 LYS cc_start: 0.9465 (tppt) cc_final: 0.8910 (mmtm)
REVERT: C  116 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8324 (ttp-110)
REVERT: C  142 TYR cc_start: 0.6930 (m-80) cc_final: 0.6388 (m-80)
REVERT: B   42 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8468 (tttt)
REVERT: B   54 ASP cc_start: 0.8531 (t0) cc_final: 0.8275 (t0)
REVERT: B  109 GLU cc_start: 0.8471 (tt0) cc_final: 0.8255 (tt0)
REVERT: B  208 ASP cc_start: 0.8640 (t0) cc_final: 0.8262 (t0)
  outliers start: 10
  outliers final: 8
  residues processed: 185
  average time/residue: 0.1499
  time to fit residues: 35.0041
Evaluate side-chains
  172 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 164
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
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 28 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 2 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9980
   chunk 103 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 38 optimal weight:    0.3980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.070767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.052409 restraints weight = 39331.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 4.38
r_work: 0.2677 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2689
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2689 r_free = 0.2689    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.1811

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= 0.134
  Angle     :  0.577   7.547  12551  Z= 0.288
  Chirality :  0.036   0.155   1470
  Planarity :  0.004   0.047   1567
  Dihedral  :  3.565  26.282   1248
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  1.90 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 12.59 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.46 (0.25), residues: 1162
  helix:  2.77 (0.16), residues: 1024
  sheet:  None (None), residues: 0
  loop : -1.87 (0.51), residues: 138

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 9270)
  covalent geometry    : angle       0.57693 (12551)
  hydrogen bonds       : bond        0.04091 (  818)
  hydrogen bonds       : angle       3.27150 ( 2455)

*********************** 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
  187 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 175
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 ASN cc_start: 0.9183 (t0) cc_final: 0.8760 (m-40)
REVERT: A  208 ASP cc_start: 0.9059 (t0) cc_final: 0.8713 (t0)
REVERT: E   49 LYS cc_start: 0.9295 (tptp) cc_final: 0.8968 (tppt)
REVERT: E   96 LYS cc_start: 0.9436 (mmmt) cc_final: 0.9155 (mtmm)
REVERT: E  208 ASP cc_start: 0.8685 (t0) cc_final: 0.8418 (t0)
REVERT: D   59 LYS cc_start: 0.9144 (mmmt) cc_final: 0.8865 (ttpp)
REVERT: D   60 MET cc_start: 0.9530 (tpp) cc_final: 0.9133 (tpp)
REVERT: D  113 ARG cc_start: 0.8493 (mmp80) cc_final: 0.8285 (mmp80)
REVERT: D  154 ASN cc_start: 0.9114 (t0) cc_final: 0.8842 (t0)
REVERT: D  208 ASP cc_start: 0.8781 (t0) cc_final: 0.8443 (t0)
REVERT: C   59 LYS cc_start: 0.9329 (pptt) cc_final: 0.9055 (pptt)
REVERT: C   88 TYR cc_start: 0.8336 (t80) cc_final: 0.7860 (t80)
REVERT: C   91 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8560 (tt)
REVERT: C   99 LYS cc_start: 0.9526 (tppt) cc_final: 0.9016 (mmtm)
REVERT: C  116 ARG cc_start: 0.9012 (ttp80) cc_final: 0.8632 (ttp-110)
REVERT: C  142 TYR cc_start: 0.7200 (m-80) cc_final: 0.6629 (m-80)
REVERT: B   42 LYS cc_start: 0.8928 (ttpt) cc_final: 0.8629 (ttpt)
REVERT: B  122 ASP cc_start: 0.9008 (t0) cc_final: 0.8625 (t0)
REVERT: B  208 ASP cc_start: 0.8869 (t0) cc_final: 0.8525 (t0)
REVERT: F   13 LYS cc_start: 0.8652 (pttp) cc_final: 0.8070 (pptt)
REVERT: G   42 MET cc_start: 0.8972 (mtp) cc_final: 0.8491 (ttm)
  outliers start: 12
  outliers final: 4
  residues processed: 185
  average time/residue: 0.1458
  time to fit residues: 34.2647
Evaluate side-chains
  170 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 165
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain B residue   31 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 16 optimal weight:    0.0470
   chunk 73 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 88 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.5880

-------------------------------------------------------------------------------
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 = 0.3292 r_free = 0.3292 target = 0.071203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.051610 restraints weight = 54236.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 5.19
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2832
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2832
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.2054

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= 0.133
  Angle     :  0.556   6.922  12551  Z= 0.280
  Chirality :  0.036   0.157   1470
  Planarity :  0.004   0.046   1567
  Dihedral  :  3.425  23.198   1248
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.64 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.88 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.70 (0.25), residues: 1162
  helix:  2.94 (0.16), residues: 1023
  sheet:  None (None), residues: 0
  loop : -1.82 (0.51), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E 113 
 TYR   0.012   0.001   TYR G  25 
 PHE   0.014   0.001   PHE D 198 
 TRP   0.007   0.001   TRP B 150 
 HIS   0.003   0.000   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9270)
  covalent geometry    : angle       0.55584 (12551)
  hydrogen bonds       : bond        0.03978 (  818)
  hydrogen bonds       : angle       3.17494 ( 2455)

*********************** 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: 18
    poor density    : 174
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A   54 ASP cc_start: 0.8694 (t0) cc_final: 0.8414 (t0)
REVERT: A  154 ASN cc_start: 0.9102 (t0) cc_final: 0.8672 (m-40)
REVERT: A  208 ASP cc_start: 0.8857 (t0) cc_final: 0.8448 (t0)
REVERT: E   49 LYS cc_start: 0.9220 (tptp) cc_final: 0.8900 (tppt)
REVERT: E   96 LYS cc_start: 0.9388 (mmmt) cc_final: 0.9058 (mtmm)
REVERT: E  208 ASP cc_start: 0.8456 (t0) cc_final: 0.8198 (t0)
REVERT: D   13 ASP cc_start: 0.9514 (m-30) cc_final: 0.8848 (t0)
REVERT: D   54 ASP cc_start: 0.9052 (t0) cc_final: 0.8842 (t0)
REVERT: D   59 LYS cc_start: 0.9174 (mmmt) cc_final: 0.8888 (ttpp)
REVERT: D   60 MET cc_start: 0.9479 (tpp) cc_final: 0.9020 (tpp)
REVERT: D   96 LYS cc_start: 0.9679 (tppp) cc_final: 0.9233 (tptp)
REVERT: D  113 ARG cc_start: 0.8550 (mmp80) cc_final: 0.8266 (mmp80)
REVERT: D  154 ASN cc_start: 0.8987 (t0) cc_final: 0.8641 (t0)
REVERT: D  208 ASP cc_start: 0.8761 (t0) cc_final: 0.8355 (t0)
REVERT: C   59 LYS cc_start: 0.9384 (pptt) cc_final: 0.9096 (pptt)
REVERT: C   99 LYS cc_start: 0.9479 (tppt) cc_final: 0.8942 (mmtm)
REVERT: C  116 ARG cc_start: 0.8785 (ttp80) cc_final: 0.8368 (ttp-110)
REVERT: C  142 TYR cc_start: 0.7053 (m-80) cc_final: 0.6443 (m-80)
REVERT: B   42 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8443 (ttpt)
REVERT: B  122 ASP cc_start: 0.8909 (t0) cc_final: 0.8464 (t0)
REVERT: B  208 ASP cc_start: 0.8671 (t0) cc_final: 0.8311 (t0)
REVERT: F   13 LYS cc_start: 0.8604 (pttp) cc_final: 0.8008 (pptt)
REVERT: G   42 MET cc_start: 0.8778 (mtp) cc_final: 0.8294 (ttm)
  outliers start: 18
  outliers final: 9
  residues processed: 186
  average time/residue: 0.1488
  time to fit residues: 34.8835
Evaluate side-chains
  173 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 164
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain C residue   45 MET
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  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 40 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 58 optimal weight:    8.9990
   chunk 47 optimal weight:    1.9990
   chunk 83 optimal weight:    0.4980
   chunk 74 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 105 optimal weight:    0.8980
   chunk 86 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0020
   overall best weight:    0.6188

-------------------------------------------------------------------------------
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 = 0.3290 r_free = 0.3290 target = 0.071104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.051717 restraints weight = 54729.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 5.17
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2834
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2834
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.2184

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= 0.135
  Angle     :  0.558   7.053  12551  Z= 0.279
  Chirality :  0.036   0.157   1470
  Planarity :  0.004   0.046   1567
  Dihedral  :  3.356  22.036   1248
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.47 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.19 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.91 (0.25), residues: 1162
  helix:  3.06 (0.16), residues: 1025
  sheet:  None (None), residues: 0
  loop : -1.65 (0.52), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 113 
 TYR   0.014   0.001   TYR C  71 
 PHE   0.014   0.001   PHE D 212 
 TRP   0.007   0.001   TRP C 150 
 HIS   0.002   0.000   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 9270)
  covalent geometry    : angle       0.55816 (12551)
  hydrogen bonds       : bond        0.03947 (  818)
  hydrogen bonds       : angle       3.13415 ( 2455)

*********************** 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
  193 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 173
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A   26 MET cc_start: 0.8841 (mtm) cc_final: 0.8600 (mpp)
REVERT: A   54 ASP cc_start: 0.8694 (t0) cc_final: 0.8439 (t0)
REVERT: A  154 ASN cc_start: 0.9122 (t0) cc_final: 0.8675 (m-40)
REVERT: A  208 ASP cc_start: 0.8875 (t0) cc_final: 0.8459 (t0)
REVERT: E   26 MET cc_start: 0.8561 (mtm) cc_final: 0.7863 (mtm)
REVERT: E   49 LYS cc_start: 0.9211 (tptp) cc_final: 0.8868 (tppt)
REVERT: E   96 LYS cc_start: 0.9370 (mmmt) cc_final: 0.9092 (mtmm)
REVERT: E  208 ASP cc_start: 0.8488 (t0) cc_final: 0.8207 (t0)
REVERT: D   13 ASP cc_start: 0.9502 (m-30) cc_final: 0.8867 (t0)
REVERT: D   54 ASP cc_start: 0.9079 (t0) cc_final: 0.8862 (t0)
REVERT: D   59 LYS cc_start: 0.9182 (mmmt) cc_final: 0.8894 (ttpp)
REVERT: D   60 MET cc_start: 0.9462 (tpp) cc_final: 0.9011 (tpp)
REVERT: D   96 LYS cc_start: 0.9674 (tppp) cc_final: 0.9248 (tptp)
REVERT: D  113 ARG cc_start: 0.8591 (mmp80) cc_final: 0.8375 (mmp80)
REVERT: D  154 ASN cc_start: 0.8988 (t0) cc_final: 0.8643 (t0)
REVERT: D  197 HIS cc_start: 0.8364 (t-90) cc_final: 0.8145 (t-170)
REVERT: D  208 ASP cc_start: 0.8778 (t0) cc_final: 0.8351 (t0)
REVERT: C   59 LYS cc_start: 0.9382 (pptt) cc_final: 0.9093 (pptt)
REVERT: C   99 LYS cc_start: 0.9477 (tppt) cc_final: 0.8940 (mmtm)
REVERT: C  116 ARG cc_start: 0.8776 (ttp80) cc_final: 0.8542 (ttp80)
REVERT: C  142 TYR cc_start: 0.7000 (m-80) cc_final: 0.6380 (m-80)
REVERT: B   42 LYS cc_start: 0.8752 (ttpt) cc_final: 0.8428 (ttpt)
REVERT: B  122 ASP cc_start: 0.8882 (t0) cc_final: 0.8410 (t0)
REVERT: B  208 ASP cc_start: 0.8679 (t0) cc_final: 0.8319 (t0)
REVERT: F   13 LYS cc_start: 0.8607 (pttp) cc_final: 0.8032 (pptt)
REVERT: G   42 MET cc_start: 0.8829 (mtp) cc_final: 0.8312 (ttm)
  outliers start: 20
  outliers final: 13
  residues processed: 186
  average time/residue: 0.1426
  time to fit residues: 33.6763
Evaluate side-chains
  178 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 165
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
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   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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 57 optimal weight:    0.4980
   chunk 73 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3281 r_free = 0.3281 target = 0.070624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.051255 restraints weight = 55062.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.2824 rms_B_bonded: 5.18
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.2282

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= 0.141
  Angle     :  0.556   6.847  12551  Z= 0.280
  Chirality :  0.036   0.151   1470
  Planarity :  0.004   0.048   1567
  Dihedral  :  3.313  20.785   1248
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.55 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.02 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.96 (0.25), residues: 1162
  helix:  3.09 (0.16), residues: 1025
  sheet:  None (None), residues: 0
  loop : -1.58 (0.52), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG E 113 
 TYR   0.014   0.001   TYR C  71 
 PHE   0.013   0.001   PHE A  57 
 TRP   0.007   0.001   TRP C 150 
 HIS   0.002   0.000   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 9270)
  covalent geometry    : angle       0.55649 (12551)
  hydrogen bonds       : bond        0.03951 (  818)
  hydrogen bonds       : angle       3.11771 ( 2455)

*********************** 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
  191 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 173
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A   54 ASP cc_start: 0.8686 (t0) cc_final: 0.8446 (t0)
REVERT: A   59 LYS cc_start: 0.9067 (tmmt) cc_final: 0.8598 (tppt)
REVERT: A  154 ASN cc_start: 0.9129 (t0) cc_final: 0.8683 (m-40)
REVERT: A  208 ASP cc_start: 0.8870 (t0) cc_final: 0.8442 (t0)
REVERT: E   49 LYS cc_start: 0.9209 (tptp) cc_final: 0.8860 (tppt)
REVERT: E   96 LYS cc_start: 0.9349 (mmmt) cc_final: 0.9098 (mtmm)
REVERT: E  208 ASP cc_start: 0.8520 (t0) cc_final: 0.8219 (t0)
REVERT: D   13 ASP cc_start: 0.9493 (m-30) cc_final: 0.8869 (t0)
REVERT: D   54 ASP cc_start: 0.9089 (t0) cc_final: 0.8872 (t0)
REVERT: D   60 MET cc_start: 0.9479 (tpp) cc_final: 0.9086 (tpp)
REVERT: D   96 LYS cc_start: 0.9682 (tppp) cc_final: 0.9278 (tptp)
REVERT: D  113 ARG cc_start: 0.8623 (mmp80) cc_final: 0.8390 (mmp80)
REVERT: D  154 ASN cc_start: 0.8967 (t0) cc_final: 0.8627 (t0)
REVERT: D  197 HIS cc_start: 0.8440 (t-90) cc_final: 0.8236 (t-170)
REVERT: D  208 ASP cc_start: 0.8811 (t0) cc_final: 0.8429 (t0)
REVERT: C   16 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8833 (mt)
REVERT: C   35 PHE cc_start: 0.8475 (t80) cc_final: 0.8241 (t80)
REVERT: C   59 LYS cc_start: 0.9368 (pptt) cc_final: 0.9075 (pptt)
REVERT: C   99 LYS cc_start: 0.9488 (tppt) cc_final: 0.8956 (mmtm)
REVERT: C  116 ARG cc_start: 0.8798 (ttp80) cc_final: 0.8406 (ttp-110)
REVERT: C  142 TYR cc_start: 0.7020 (m-80) cc_final: 0.6402 (m-80)
REVERT: B   42 LYS cc_start: 0.8756 (ttpt) cc_final: 0.8441 (ttpt)
REVERT: B  122 ASP cc_start: 0.8892 (t0) cc_final: 0.8413 (t0)
REVERT: B  208 ASP cc_start: 0.8713 (t0) cc_final: 0.8363 (t0)
REVERT: F   13 LYS cc_start: 0.8622 (pttp) cc_final: 0.8038 (pptt)
  outliers start: 18
  outliers final: 13
  residues processed: 186
  average time/residue: 0.1514
  time to fit residues: 35.6930
Evaluate side-chains
  179 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 165
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 86 optimal weight:    0.0040
   chunk 67 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 55 optimal weight:    0.5980
   chunk 101 optimal weight:    0.9990
   chunk 109 optimal weight:    0.6980
   chunk 108 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 59 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.4992

-------------------------------------------------------------------------------
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 = 0.3293 r_free = 0.3293 target = 0.071261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.053031 restraints weight = 34801.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 4.11
r_work: 0.2693 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2716
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2716
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.2368

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= 0.128
  Angle     :  0.558   7.108  12551  Z= 0.280
  Chirality :  0.035   0.162   1470
  Planarity :  0.004   0.053   1567
  Dihedral  :  3.295  19.825   1248
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.55 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 16.65 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.06 (0.25), residues: 1162
  helix:  3.16 (0.16), residues: 1021
  sheet:  None (None), residues: 0
  loop : -1.39 (0.52), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG E 113 
 TYR   0.018   0.001   TYR B  38 
 PHE   0.012   0.001   PHE A  57 
 TRP   0.006   0.001   TRP C 150 
 HIS   0.002   0.000   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9270)
  covalent geometry    : angle       0.55813 (12551)
  hydrogen bonds       : bond        0.03880 (  818)
  hydrogen bonds       : angle       3.09543 ( 2455)

*********************** 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
  190 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 173
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A   26 MET cc_start: 0.8942 (mtm) cc_final: 0.8329 (mpp)
REVERT: A   59 LYS cc_start: 0.9090 (tmmt) cc_final: 0.8618 (tppt)
REVERT: A  154 ASN cc_start: 0.9198 (t0) cc_final: 0.8737 (m-40)
REVERT: A  208 ASP cc_start: 0.9082 (t0) cc_final: 0.8731 (t0)
REVERT: E   26 MET cc_start: 0.8986 (mtm) cc_final: 0.8662 (mtm)
REVERT: E   96 LYS cc_start: 0.9348 (mmmt) cc_final: 0.9102 (mtmm)
REVERT: E  208 ASP cc_start: 0.8675 (t0) cc_final: 0.8425 (t0)
REVERT: D   13 ASP cc_start: 0.9509 (m-30) cc_final: 0.8901 (t0)
REVERT: D   54 ASP cc_start: 0.9150 (t0) cc_final: 0.8939 (t0)
REVERT: D   59 LYS cc_start: 0.9202 (tppt) cc_final: 0.8870 (ttpp)
REVERT: D   60 MET cc_start: 0.9510 (tpp) cc_final: 0.9086 (tpp)
REVERT: D   96 LYS cc_start: 0.9654 (tppp) cc_final: 0.9227 (tptp)
REVERT: D  113 ARG cc_start: 0.8622 (mmp80) cc_final: 0.8368 (mmp80)
REVERT: D  154 ASN cc_start: 0.9130 (t0) cc_final: 0.8869 (t0)
REVERT: D  208 ASP cc_start: 0.8890 (t0) cc_final: 0.8536 (t0)
REVERT: C   16 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.8952 (mt)
REVERT: C   35 PHE cc_start: 0.8560 (t80) cc_final: 0.8305 (t80)
REVERT: C   59 LYS cc_start: 0.9312 (pptt) cc_final: 0.9024 (pptt)
REVERT: C   71 TYR cc_start: 0.8695 (t80) cc_final: 0.8445 (t80)
REVERT: C   99 LYS cc_start: 0.9527 (tppt) cc_final: 0.8974 (mmtm)
REVERT: C  116 ARG cc_start: 0.9026 (ttp80) cc_final: 0.8817 (ttp80)
REVERT: C  142 TYR cc_start: 0.7246 (m-80) cc_final: 0.6653 (m-80)
REVERT: B   42 LYS cc_start: 0.8915 (ttpt) cc_final: 0.8641 (ttpt)
REVERT: B   60 MET cc_start: 0.9341 (ttp) cc_final: 0.8921 (tpp)
REVERT: B  208 ASP cc_start: 0.8854 (t0) cc_final: 0.8542 (t0)
REVERT: F   13 LYS cc_start: 0.8696 (pttp) cc_final: 0.8140 (pptt)
  outliers start: 17
  outliers final: 12
  residues processed: 186
  average time/residue: 0.1549
  time to fit residues: 36.1399
Evaluate side-chains
  177 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 164
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain C residue   10 HIS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 82 optimal weight:    0.6980
   chunk 85 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 110 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 106 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0970
   overall best weight:    0.6578

-------------------------------------------------------------------------------
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 = 0.3286 r_free = 0.3286 target = 0.070859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.051112 restraints weight = 63583.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.2818 rms_B_bonded: 5.57
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2820
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2820 r_free = 0.2820    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2820 r_free = 0.2820    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2820
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.2444

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= 0.138
  Angle     :  0.567   9.644  12551  Z= 0.283
  Chirality :  0.036   0.156   1470
  Planarity :  0.004   0.057   1567
  Dihedral  :  3.266  18.849   1248
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.55 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.48 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.08 (0.25), residues: 1162
  helix:  3.16 (0.16), residues: 1021
  sheet:  None (None), residues: 0
  loop : -1.34 (0.53), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E 113 
 TYR   0.014   0.001   TYR B  38 
 PHE   0.013   0.001   PHE A  57 
 TRP   0.007   0.001   TRP C 150 
 HIS   0.002   0.000   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9270)
  covalent geometry    : angle       0.56689 (12551)
  hydrogen bonds       : bond        0.03913 (  818)
  hydrogen bonds       : angle       3.10123 ( 2455)

*********************** 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
  184 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 166
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A   54 ASP cc_start: 0.8658 (t0) cc_final: 0.8399 (t0)
REVERT: A   59 LYS cc_start: 0.9070 (tmmt) cc_final: 0.8618 (tppt)
REVERT: A  154 ASN cc_start: 0.9149 (t0) cc_final: 0.8678 (m-40)
REVERT: A  208 ASP cc_start: 0.8859 (t0) cc_final: 0.8465 (t0)
REVERT: E   26 MET cc_start: 0.8597 (mtm) cc_final: 0.8035 (mtm)
REVERT: E   96 LYS cc_start: 0.9304 (mmmt) cc_final: 0.9045 (mtmm)
REVERT: E  208 ASP cc_start: 0.8508 (t0) cc_final: 0.8231 (t0)
REVERT: D   13 ASP cc_start: 0.9484 (m-30) cc_final: 0.8877 (t0)
REVERT: D   59 LYS cc_start: 0.9250 (tppt) cc_final: 0.8885 (ttpp)
REVERT: D   60 MET cc_start: 0.9491 (tpp) cc_final: 0.9054 (tpp)
REVERT: D   96 LYS cc_start: 0.9651 (tppp) cc_final: 0.9252 (tptp)
REVERT: D  100 ARG cc_start: 0.8708 (mmp80) cc_final: 0.8263 (mmp80)
REVERT: D  113 ARG cc_start: 0.8642 (mmp80) cc_final: 0.8383 (mmp80)
REVERT: D  208 ASP cc_start: 0.8850 (t0) cc_final: 0.8440 (t0)
REVERT: C   16 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8904 (mt)
REVERT: C   35 PHE cc_start: 0.8460 (t80) cc_final: 0.8218 (t80)
REVERT: C   59 LYS cc_start: 0.9379 (pptt) cc_final: 0.9088 (pptt)
REVERT: C   73 ASN cc_start: 0.9512 (m110) cc_final: 0.9244 (p0)
REVERT: C   99 LYS cc_start: 0.9486 (tppt) cc_final: 0.8915 (mmtm)
REVERT: C  116 ARG cc_start: 0.8819 (ttp80) cc_final: 0.8562 (ttp80)
REVERT: C  142 TYR cc_start: 0.7044 (m-80) cc_final: 0.6421 (m-80)
REVERT: C  222 ARG cc_start: 0.8894 (ttp80) cc_final: 0.8599 (tmm160)
REVERT: B   42 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8436 (ttpt)
REVERT: B   60 MET cc_start: 0.9121 (ttp) cc_final: 0.8785 (tpp)
REVERT: B  208 ASP cc_start: 0.8711 (t0) cc_final: 0.8382 (t0)
REVERT: F   13 LYS cc_start: 0.8624 (pttp) cc_final: 0.8029 (pptt)
REVERT: G   42 MET cc_start: 0.8846 (mtp) cc_final: 0.8338 (ttm)
  outliers start: 18
  outliers final: 15
  residues processed: 179
  average time/residue: 0.1519
  time to fit residues: 34.3169
Evaluate side-chains
  179 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 163
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain C residue   10 HIS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  163 ASP
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain G residue   43 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 83 optimal weight:    0.7980
   chunk 104 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0980
   chunk 70 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 110 optimal weight:    0.0020
   chunk 23 optimal weight:    0.7980
   chunk 52 optimal weight:    0.4980
   overall best weight:    0.3588

-------------------------------------------------------------------------------
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 = 0.3307 r_free = 0.3307 target = 0.072041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.052672 restraints weight = 56557.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 5.24
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2856
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    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 = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2856
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.2546

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= 0.124
  Angle     :  0.566   8.553  12551  Z= 0.283
  Chirality :  0.035   0.158   1470
  Planarity :  0.004   0.056   1567
  Dihedral  :  3.231  17.562   1248
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.64 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 18.31 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.17 (0.25), residues: 1162
  helix:  3.23 (0.16), residues: 1021
  sheet:  None (None), residues: 0
  loop : -1.38 (0.53), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG E 113 
 TYR   0.014   0.001   TYR B  38 
 PHE   0.011   0.001   PHE A  57 
 TRP   0.006   0.001   TRP B 150 
 HIS   0.002   0.000   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9270)
  covalent geometry    : angle       0.56552 (12551)
  hydrogen bonds       : bond        0.03783 (  818)
  hydrogen bonds       : angle       3.04509 ( 2455)

*********************** 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
  183 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 169
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A   54 ASP cc_start: 0.8685 (t0) cc_final: 0.8430 (t0)
REVERT: A   59 LYS cc_start: 0.9047 (tmmt) cc_final: 0.8620 (tppt)
REVERT: A  154 ASN cc_start: 0.9134 (t0) cc_final: 0.8666 (m-40)
REVERT: A  208 ASP cc_start: 0.8846 (t0) cc_final: 0.8448 (t0)
REVERT: A  222 ARG cc_start: 0.9100 (ttp-110) cc_final: 0.8853 (ttp-110)
REVERT: E   26 MET cc_start: 0.8589 (mtm) cc_final: 0.7962 (mtm)
REVERT: E   42 LYS cc_start: 0.9010 (ttpp) cc_final: 0.8674 (ttpp)
REVERT: E   59 LYS cc_start: 0.8534 (pttm) cc_final: 0.8319 (pttm)
REVERT: E   60 MET cc_start: 0.9238 (tpp) cc_final: 0.9001 (tpp)
REVERT: E   96 LYS cc_start: 0.9301 (mmmt) cc_final: 0.9044 (mtmm)
REVERT: E  208 ASP cc_start: 0.8463 (t0) cc_final: 0.8198 (t0)
REVERT: D   13 ASP cc_start: 0.9476 (m-30) cc_final: 0.8893 (t0)
REVERT: D   59 LYS cc_start: 0.9243 (tppt) cc_final: 0.8858 (ttpp)
REVERT: D   60 MET cc_start: 0.9460 (tpp) cc_final: 0.9031 (tpp)
REVERT: D   96 LYS cc_start: 0.9639 (tppp) cc_final: 0.9233 (tptp)
REVERT: D  100 ARG cc_start: 0.8735 (mmp80) cc_final: 0.8288 (mmp80)
REVERT: D  113 ARG cc_start: 0.8648 (mmp80) cc_final: 0.8380 (mmp80)
REVERT: D  208 ASP cc_start: 0.8737 (t0) cc_final: 0.8441 (t0)
REVERT: C   16 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8932 (mt)
REVERT: C   35 PHE cc_start: 0.8447 (t80) cc_final: 0.8194 (t80)
REVERT: C   73 ASN cc_start: 0.9508 (m110) cc_final: 0.9270 (p0)
REVERT: C  116 ARG cc_start: 0.8788 (ttp80) cc_final: 0.8550 (ttp80)
REVERT: C  142 TYR cc_start: 0.6967 (m-80) cc_final: 0.6379 (m-80)
REVERT: B   42 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8451 (ttpt)
REVERT: B   60 MET cc_start: 0.9101 (ttp) cc_final: 0.8768 (tpp)
REVERT: B  208 ASP cc_start: 0.8678 (t0) cc_final: 0.8397 (t0)
REVERT: F   13 LYS cc_start: 0.8591 (pttp) cc_final: 0.8021 (pptt)
REVERT: G   42 MET cc_start: 0.8807 (mtp) cc_final: 0.8287 (ttm)
  outliers start: 14
  outliers final: 12
  residues processed: 181
  average time/residue: 0.1519
  time to fit residues: 34.7158
Evaluate side-chains
  177 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 164
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain E residue  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 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 5 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 99 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3310 r_free = 0.3310 target = 0.071639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.052277 restraints weight = 54450.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 5.09
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2871
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    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 = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2871
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.2603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9270  Z= 0.145
  Angle     :  0.586   8.229  12551  Z= 0.294
  Chirality :  0.036   0.157   1470
  Planarity :  0.004   0.064   1567
  Dihedral  :  3.201  17.015   1248
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.47 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 18.83 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.09 (0.25), residues: 1162
  helix:  3.17 (0.16), residues: 1022
  sheet:  None (None), residues: 0
  loop : -1.31 (0.54), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG E 113 
 TYR   0.014   0.001   TYR B  38 
 PHE   0.014   0.001   PHE A  57 
 TRP   0.008   0.001   TRP C 150 
 HIS   0.002   0.000   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 9270)
  covalent geometry    : angle       0.58615 (12551)
  hydrogen bonds       : bond        0.03917 (  818)
  hydrogen bonds       : angle       3.09719 ( 2455)

********************** 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
  174 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 160
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A   54 ASP cc_start: 0.8698 (t0) cc_final: 0.8425 (t0)
REVERT: A   59 LYS cc_start: 0.9058 (tmmt) cc_final: 0.8612 (tppt)
REVERT: A  154 ASN cc_start: 0.9146 (t0) cc_final: 0.8687 (m-40)
REVERT: A  208 ASP cc_start: 0.8865 (t0) cc_final: 0.8464 (t0)
REVERT: E   26 MET cc_start: 0.8605 (mtm) cc_final: 0.7987 (mtm)
REVERT: E   96 LYS cc_start: 0.9297 (mmmt) cc_final: 0.9059 (mtmm)
REVERT: E  208 ASP cc_start: 0.8516 (t0) cc_final: 0.8240 (t0)
REVERT: D   13 ASP cc_start: 0.9494 (m-30) cc_final: 0.8892 (t0)
REVERT: D   60 MET cc_start: 0.9464 (tpp) cc_final: 0.9088 (tpp)
REVERT: D   96 LYS cc_start: 0.9637 (tppp) cc_final: 0.9235 (tptp)
REVERT: D  100 ARG cc_start: 0.8755 (mmp80) cc_final: 0.8277 (mmp80)
REVERT: D  113 ARG cc_start: 0.8641 (mmp80) cc_final: 0.8354 (mmp80)
REVERT: D  208 ASP cc_start: 0.8824 (t0) cc_final: 0.8468 (t0)
REVERT: C   16 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.8941 (mt)
REVERT: C   35 PHE cc_start: 0.8495 (t80) cc_final: 0.8241 (t80)
REVERT: C   72 ASN cc_start: 0.9467 (m110) cc_final: 0.9170 (m110)
REVERT: C  116 ARG cc_start: 0.8804 (ttp80) cc_final: 0.8556 (ttp80)
REVERT: C  142 TYR cc_start: 0.6985 (m-80) cc_final: 0.6383 (m-80)
REVERT: B   42 LYS cc_start: 0.8774 (ttpt) cc_final: 0.8472 (ttpt)
REVERT: B   60 MET cc_start: 0.9106 (ttp) cc_final: 0.8790 (tpp)
REVERT: B  208 ASP cc_start: 0.8706 (t0) cc_final: 0.8452 (t0)
REVERT: F   13 LYS cc_start: 0.8623 (pttp) cc_final: 0.8017 (pptt)
REVERT: G   42 MET cc_start: 0.8831 (mtp) cc_final: 0.8260 (ttm)
  outliers start: 14
  outliers final: 13
  residues processed: 171
  average time/residue: 0.1487
  time to fit residues: 32.2780
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  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain D residue  130 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 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 47 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0270
   chunk 83 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 28 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.5438

-------------------------------------------------------------------------------
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**
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 = 0.3315 r_free = 0.3315 target = 0.071877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.052773 restraints weight = 47035.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 4.75
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2886
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2886
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9270  Z= 0.135
  Angle     :  0.591   8.000  12551  Z= 0.295
  Chirality :  0.036   0.161   1470
  Planarity :  0.004   0.063   1567
  Dihedral  :  3.208  16.304   1248
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.55 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 18.73 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.08 (0.25), residues: 1162
  helix:  3.18 (0.16), residues: 1019
  sheet:  None (None), residues: 0
  loop : -1.36 (0.53), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG E 113 
 TYR   0.013   0.001   TYR B  38 
 PHE   0.013   0.001   PHE A  57 
 TRP   0.006   0.001   TRP C 150 
 HIS   0.002   0.000   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 9270)
  covalent geometry    : angle       0.59087 (12551)
  hydrogen bonds       : bond        0.03848 (  818)
  hydrogen bonds       : angle       3.08133 ( 2455)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2126.39 seconds
wall clock time: 37 minutes 21.55 seconds (2241.55 seconds total)