Starting phenix.real_space_refine
on Wed Feb 12 03:59:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qnu_4609/02_2025/6qnu_4609.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qnu_4609/02_2025/6qnu_4609.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qnu_4609/02_2025/6qnu_4609.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qnu_4609/02_2025/6qnu_4609.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qnu_4609/02_2025/6qnu_4609.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qnu_4609/02_2025/6qnu_4609.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    4655      2.51       5
     N    1169      2.21       5
     O    1404      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7250
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 1400
          Classifications: {'peptide': 178}
          Link IDs: {'PTRANS': 10, 'TRANS': 167}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 181, 1424
          Classifications: {'peptide': 181}
          Link IDs: {'PTRANS': 11, 'TRANS': 169}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 179, 1409
          Classifications: {'peptide': 179}
          Link IDs: {'PTRANS': 10, 'TRANS': 168}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 1541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1541
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 7, 'TRANS': 187}
          Chain breaks: 4
    Chain: "E"
      Number of atoms: 1476
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1476
          Classifications: {'peptide': 187}
          Link IDs: {'PTRANS': 7, 'TRANS': 179}
          Chain breaks: 5
  Time building chain proxies: 2.31, per 1000 atoms: 0.32
  Number of scatterers: 7250
  At special positions: 0
  Unit cell: (94.963, 105.633, 93.896, 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      22     16.00
     O    1404      8.00
     N    1169      7.00
     C    4655      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: 1.93
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1742

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 17 sheets defined
      2.8% alpha, 33.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 177 through 182
    Processing helix  chain 'B' and resid 177 through 182
      removed outlier: 3.583A  pdb=" N   ASN B 181 " --> pdb=" O   SER B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 186
    Processing helix  chain 'C' and resid 226 through 230
      removed outlier: 4.153A  pdb=" N   PHE C 229 " --> pdb=" O   ALA C 226 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 266 through 270
      removed outlier: 4.424A  pdb=" N   GLY E 269 " --> pdb=" O   GLY E 266 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 197
      removed outlier: 3.508A  pdb=" N   VAL A 269 " --> pdb=" O   GLY A 253 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 132 through 133
    Processing sheet with id=AA4, first strand: chain 'B' and resid 188 through 196
      removed outlier: 3.734A  pdb=" N   LEU B 289 " --> pdb=" O   THR B 270 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   ASN B 293 " --> pdb=" O   PRO B 266 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 132 through 133
      removed outlier: 4.175A  pdb=" N   LEU C 305 " --> pdb=" O   GLY C 175 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 132 through 133
      removed outlier: 3.652A  pdb=" N   PHE C 312 " --> pdb=" O   GLY C 169 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 188 through 197
      removed outlier: 5.542A  pdb=" N   ASN C 293 " --> pdb=" O   PRO C 266 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 114 through 120
      removed outlier: 6.401A  pdb=" N   PHE D 115 " --> pdb=" O   GLN D 210 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   ARG D 212 " --> pdb=" O   PHE D 115 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   GLY D 117 " --> pdb=" O   ARG D 212 " (cutoff:3.500A)
      removed outlier: 7.397A  pdb=" N   LEU D 214 " --> pdb=" O   GLY D 117 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   VAL D 119 " --> pdb=" O   LEU D 214 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   GLU D 191 " --> pdb=" O   ILE D 151 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   ILE D 151 " --> pdb=" O   GLU D 191 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   ARG D 193 " --> pdb=" O   TYR D 149 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   TYR D 149 " --> pdb=" O   ARG D 193 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 128 through 131
      removed outlier: 6.854A  pdb=" N   ILE D 171 " --> pdb=" O   VAL D 129 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLU D 170 " --> pdb=" O   ASN D 165 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 222 through 223
      removed outlier: 3.722A  pdb=" N   VAL D 222 " --> pdb=" O   PHE D 247 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   GLU D 240 " --> pdb=" O   LEU D 287 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   LEU D 287 " --> pdb=" O   GLU D 240 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   THR D 242 " --> pdb=" O   VAL D 285 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 259 through 263
      removed outlier: 3.753A  pdb=" N   VAL D 303 " --> pdb=" O   ILE D 324 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ILE D 324 " --> pdb=" O   VAL D 303 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 114 through 120
      removed outlier: 6.511A  pdb=" N   PHE E 115 " --> pdb=" O   GLN E 210 " (cutoff:3.500A)
      removed outlier: 7.633A  pdb=" N   ARG E 212 " --> pdb=" O   PHE E 115 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   GLY E 117 " --> pdb=" O   ARG E 212 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   LEU E 214 " --> pdb=" O   GLY E 117 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   VAL E 119 " --> pdb=" O   LEU E 214 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL E 190 " --> pdb=" O   ALA E 207 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   THR E 187 " --> pdb=" O   LEU E 154 " (cutoff:3.500A)
      removed outlier: 5.013A  pdb=" N   LEU E 154 " --> pdb=" O   THR E 187 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   THR E 189 " --> pdb=" O   VAL E 152 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 131
      removed outlier: 6.724A  pdb=" N   ILE E 171 " --> pdb=" O   VAL E 129 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 222 through 223
      removed outlier: 3.521A  pdb=" N   VAL E 222 " --> pdb=" O   PHE E 247 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 229 through 232
      removed outlier: 6.681A  pdb=" N   GLY E 230 " --> pdb=" O   LYS E 329 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 259 through 261
    Processing sheet with id=AB8, first strand: chain 'E' and resid 272 through 277

    188 hydrogen bonds defined for protein.
    507 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: 1.89

  Time building geometry restraints manager: 2.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2260
        1.34 -     1.46: 1349
        1.46 -     1.57: 3752
        1.57 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 7399
  Sorted by residual:
  bond pdb=" C   GLU E 155 "
       pdb=" N   PRO E 156 "
    ideal  model  delta    sigma   weight residual
    1.334  1.379 -0.045 2.34e-02 1.83e+03 3.68e+00
  bond pdb=" C   GLU D 155 "
       pdb=" N   PRO D 156 "
    ideal  model  delta    sigma   weight residual
    1.334  1.377 -0.043 2.34e-02 1.83e+03 3.44e+00
  bond pdb=" CA  THR A 304 "
       pdb=" CB  THR A 304 "
    ideal  model  delta    sigma   weight residual
    1.530  1.559 -0.029 1.69e-02 3.50e+03 2.95e+00
  bond pdb=" CA  TYR D 158 "
       pdb=" C   TYR D 158 "
    ideal  model  delta    sigma   weight residual
    1.524  1.540 -0.016 1.26e-02 6.30e+03 1.64e+00
  bond pdb=" CA  TYR E 158 "
       pdb=" C   TYR E 158 "
    ideal  model  delta    sigma   weight residual
    1.524  1.540 -0.016 1.26e-02 6.30e+03 1.63e+00
  ... (remaining 7394 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 9719
        2.17 -     4.34: 270
        4.34 -     6.51: 39
        6.51 -     8.68: 18
        8.68 -    10.85: 4
  Bond angle restraints: 10050
  Sorted by residual:
  angle pdb=" C   ALA A 303 "
        pdb=" N   THR A 304 "
        pdb=" CA  THR A 304 "
      ideal   model   delta    sigma   weight residual
     121.54  129.81   -8.27 1.91e+00 2.74e-01 1.88e+01
  angle pdb=" C   ASN D 219 "
        pdb=" N   ILE D 220 "
        pdb=" CA  ILE D 220 "
      ideal   model   delta    sigma   weight residual
     122.13  130.06   -7.93 1.85e+00 2.92e-01 1.84e+01
  angle pdb=" N   ILE D 315 "
        pdb=" CA  ILE D 315 "
        pdb=" C   ILE D 315 "
      ideal   model   delta    sigma   weight residual
     113.71  109.68    4.03 9.50e-01 1.11e+00 1.80e+01
  angle pdb=" C   ASP D 218 "
        pdb=" N   ASN D 219 "
        pdb=" CA  ASN D 219 "
      ideal   model   delta    sigma   weight residual
     121.54  129.22   -7.68 1.91e+00 2.74e-01 1.62e+01
  angle pdb=" N   TRP D 257 "
        pdb=" CA  TRP D 257 "
        pdb=" C   TRP D 257 "
      ideal   model   delta    sigma   weight residual
     114.04  109.06    4.98 1.24e+00 6.50e-01 1.62e+01
  ... (remaining 10045 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.84: 3940
       16.84 -    33.69: 390
       33.69 -    50.53: 66
       50.53 -    67.37: 11
       67.37 -    84.22: 6
  Dihedral angle restraints: 4413
    sinusoidal: 1724
      harmonic: 2689
  Sorted by residual:
  dihedral pdb=" CA  LEU A 273 "
           pdb=" C   LEU A 273 "
           pdb=" N   ASN A 274 "
           pdb=" CA  ASN A 274 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.37  -41.63     0      5.00e+00 4.00e-02 6.93e+01
  dihedral pdb=" CA  LEU B 273 "
           pdb=" C   LEU B 273 "
           pdb=" N   ASN B 274 "
           pdb=" CA  ASN B 274 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.15  -34.85     0      5.00e+00 4.00e-02 4.86e+01
  dihedral pdb=" CA  ASP D 218 "
           pdb=" C   ASP D 218 "
           pdb=" N   ASN D 219 "
           pdb=" CA  ASN D 219 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.28  -34.72     0      5.00e+00 4.00e-02 4.82e+01
  ... (remaining 4410 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 845
       0.053 -    0.106: 236
       0.106 -    0.159: 77
       0.159 -    0.211: 7
       0.211 -    0.264: 5
  Chirality restraints: 1170
  Sorted by residual:
  chirality pdb=" CA  TYR E 158 "
            pdb=" N   TYR E 158 "
            pdb=" C   TYR E 158 "
            pdb=" CB  TYR E 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CA  TYR D 158 "
            pdb=" N   TYR D 158 "
            pdb=" C   TYR D 158 "
            pdb=" CB  TYR D 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CB  ILE C 306 "
            pdb=" CA  ILE C 306 "
            pdb=" CG1 ILE C 306 "
            pdb=" CG2 ILE C 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.41e+00
  ... (remaining 1167 not shown)

  Planarity restraints: 1269
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 275 "    0.013 2.00e-02 2.50e+03   2.57e-02 6.60e+00
        pdb=" C   LYS B 275 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   LYS B 275 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ARG B 276 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN E 219 "   -0.011 2.00e-02 2.50e+03   2.28e-02 5.22e+00
        pdb=" C   ASN E 219 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ASN E 219 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ILE E 220 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 308 "   -0.036 5.00e-02 4.00e+02   5.37e-02 4.61e+00
        pdb=" N   PRO A 309 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 309 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 309 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1266 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 2300
        2.84 -     3.35: 5486
        3.35 -     3.87: 11611
        3.87 -     4.38: 12135
        4.38 -     4.90: 22568
  Nonbonded interactions: 54100
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 257 "
            pdb=" OE2 GLU B 299 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" OE1 GLU C 194 "
            pdb=" OH  TYR C 196 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OG1 THR C 135 "
            pdb=" O   LEU C 158 "
     model   vdw
     2.349 3.040
  nonbonded pdb=" O   LEU A 204 "
            pdb=" OG  SER A 208 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" OE1 GLU E 170 "
            pdb=" OH  TYR E 172 "
     model   vdw
     2.392 3.040
  ... (remaining 54095 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'
  selection = (chain 'B' and (resid 130 through 218 or resid 225 through 239 or resid 245 thro \ 
ugh 318))
  selection = (chain 'C' and (resid 130 through 218 or resid 225 through 318))
}
ncs_group {
  reference = (chain 'D' and (resid 108 through 134 or resid 146 through 193 or resid 206 thro \ 
ugh 233 or resid 238 through 291 or resid 299 through 331))
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     20.490
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
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      :  0.004   0.045   7399  Z= 0.286
  Angle     :  0.909  10.852  10050  Z= 0.494
  Chirality :  0.057   0.264   1170
  Planarity :  0.006   0.054   1269
  Dihedral  : 13.913  84.215   2671
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  5.89 %
    Favored  : 93.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.47 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.05 (0.24), residues: 880
  helix: -4.32 (0.26), residues: 24
  sheet: -1.61 (0.27), residues: 323
  loop : -3.50 (0.21), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 134 
 HIS   0.005   0.001   HIS B 246 
 PHE   0.019   0.002   PHE D 301 
 TYR   0.022   0.002   TYR A 170 
 ARG   0.004   0.001   ARG E 316 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 182
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
REVERT: A  162 LYS cc_start: 0.8376 (mttt) cc_final: 0.8081 (mtpp)
REVERT: A  163 ASN cc_start: 0.8567 (t0) cc_final: 0.8292 (t0)
REVERT: B  150 GLN cc_start: 0.8680 (mp-120) cc_final: 0.8340 (mt0)
REVERT: D  112 GLN cc_start: 0.7803 (mt0) cc_final: 0.7533 (tt0)
REVERT: D  164 LEU cc_start: 0.8552 (tp) cc_final: 0.8283 (tp)
REVERT: E  208 GLN cc_start: 0.7162 (mt0) cc_final: 0.6729 (mt0)
  outliers start: 5
  outliers final: 2
  residues processed: 187
  average time/residue: 0.2609
  time to fit residues: 60.7234
Evaluate side-chains
  124 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 122
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain E residue  286 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 67 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 69 optimal weight:    7.9990
   chunk 26 optimal weight:    0.5980
   chunk 42 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 80 optimal weight:    4.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 130 ASN
A 151 ASN
A 168 ASN
A 246 HIS
A 249 ASN
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 ASN
** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 168 ASN
C 249 ASN
D 208 GLN
D 210 GLN
D 236 GLN
E 126 HIS
E 183 HIS
E 217 ASN
E 312 HIS

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.155733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.135086 restraints weight = 10779.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.138375 restraints weight = 6111.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.140520 restraints weight = 4111.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7399  Z= 0.236
  Angle     :  0.627   6.671  10050  Z= 0.326
  Chirality :  0.045   0.179   1170
  Planarity :  0.004   0.037   1269
  Dihedral  :  5.976  30.901    973
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.88 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.34 (0.26), residues: 880
  helix: -2.59 (0.70), residues: 19
  sheet: -1.52 (0.26), residues: 356
  loop : -2.82 (0.24), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 134 
 HIS   0.011   0.001   HIS B 246 
 PHE   0.009   0.001   PHE D 301 
 TYR   0.016   0.001   TYR A 170 
 ARG   0.005   0.001   ARG E 180 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.792 
Fit side-chains
REVERT: A  162 LYS cc_start: 0.8273 (mttt) cc_final: 0.7839 (mtpp)
REVERT: A  163 ASN cc_start: 0.8661 (t0) cc_final: 0.8397 (t0)
REVERT: B  150 GLN cc_start: 0.8317 (mp-120) cc_final: 0.8045 (mt0)
REVERT: C  147 TYR cc_start: 0.6046 (t80) cc_final: 0.5384 (t80)
REVERT: C  314 TYR cc_start: 0.8500 (p90) cc_final: 0.8214 (p90)
REVERT: D  112 GLN cc_start: 0.7786 (mt0) cc_final: 0.7295 (tt0)
REVERT: E  166 LYS cc_start: 0.8350 (mmtm) cc_final: 0.7533 (ttmt)
REVERT: E  257 TRP cc_start: 0.8463 (OUTLIER) cc_final: 0.7811 (t-100)
  outliers start: 19
  outliers final: 10
  residues processed: 142
  average time/residue: 0.2092
  time to fit residues: 38.7832
Evaluate side-chains
  127 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain C residue  130 ASN
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  179 ASP
Chi-restraints excluded: chain D residue  183 HIS
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  241 VAL
Chi-restraints excluded: chain E residue  257 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 47 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   chunk 74 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 246 HIS
E 126 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.153936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.133071 restraints weight = 10882.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.136424 restraints weight = 6142.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.138439 restraints weight = 4125.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7399  Z= 0.256
  Angle     :  0.627   8.703  10050  Z= 0.323
  Chirality :  0.046   0.166   1170
  Planarity :  0.004   0.031   1269
  Dihedral  :  5.761  30.179    972
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 14.23 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.99 (0.26), residues: 880
  helix: -1.81 (0.87), residues: 19
  sheet: -1.35 (0.27), residues: 358
  loop : -2.55 (0.25), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 134 
 HIS   0.006   0.001   HIS B 246 
 PHE   0.018   0.002   PHE E 247 
 TYR   0.019   0.002   TYR B 179 
 ARG   0.004   0.001   ARG E 180 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.827 
Fit side-chains
REVERT: A  162 LYS cc_start: 0.8306 (mttt) cc_final: 0.7866 (mtpp)
REVERT: A  163 ASN cc_start: 0.8651 (t0) cc_final: 0.8367 (t0)
REVERT: B  150 GLN cc_start: 0.8378 (mp-120) cc_final: 0.8087 (mt0)
REVERT: B  213 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8330 (m-30)
REVERT: C  147 TYR cc_start: 0.5723 (t80) cc_final: 0.5150 (t80)
REVERT: C  314 TYR cc_start: 0.8532 (p90) cc_final: 0.8276 (p90)
REVERT: D  112 GLN cc_start: 0.7778 (mt0) cc_final: 0.7512 (tt0)
  outliers start: 25
  outliers final: 17
  residues processed: 138
  average time/residue: 0.2022
  time to fit residues: 37.0095
Evaluate side-chains
  135 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain B residue  213 ASP
Chi-restraints excluded: chain C residue  130 ASN
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain C residue  215 GLU
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  179 ASP
Chi-restraints excluded: chain D residue  183 HIS
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  250 ASP
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  241 VAL
Chi-restraints excluded: chain E residue  273 HIS
Chi-restraints excluded: chain E residue  286 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 72 optimal weight:    9.9990
   chunk 22 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 65 optimal weight:    0.3980
   chunk 43 optimal weight:    5.9990
   chunk 69 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 79 optimal weight:    0.0770
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.160261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.139445 restraints weight = 10740.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.142831 restraints weight = 6035.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.144910 restraints weight = 4040.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7399  Z= 0.149
  Angle     :  0.550   6.203  10050  Z= 0.283
  Chirality :  0.044   0.158   1170
  Planarity :  0.003   0.028   1269
  Dihedral  :  5.139  24.762    972
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.34 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.27), residues: 880
  helix: -1.43 (0.90), residues: 19
  sheet: -1.13 (0.27), residues: 357
  loop : -2.34 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP E 257 
 HIS   0.003   0.001   HIS E 126 
 PHE   0.018   0.001   PHE D 247 
 TYR   0.013   0.001   TYR A 170 
 ARG   0.006   0.001   ARG B 276 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.810 
Fit side-chains
REVERT: A  163 ASN cc_start: 0.8597 (t0) cc_final: 0.8300 (t0)
REVERT: B  150 GLN cc_start: 0.8386 (mp-120) cc_final: 0.8080 (mt0)
REVERT: C  147 TYR cc_start: 0.5511 (t80) cc_final: 0.4962 (t80)
REVERT: C  314 TYR cc_start: 0.8492 (p90) cc_final: 0.8259 (p90)
REVERT: E  133 ASN cc_start: 0.7901 (p0) cc_final: 0.7594 (m-40)
REVERT: E  166 LYS cc_start: 0.8214 (mmtm) cc_final: 0.7507 (ttmm)
REVERT: E  257 TRP cc_start: 0.8651 (OUTLIER) cc_final: 0.8034 (t-100)
REVERT: E  277 ASP cc_start: 0.7040 (t0) cc_final: 0.6828 (t0)
  outliers start: 20
  outliers final: 12
  residues processed: 150
  average time/residue: 0.2019
  time to fit residues: 39.8796
Evaluate side-chains
  131 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  250 ASP
Chi-restraints excluded: chain E residue  165 ASN
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  257 TRP
Chi-restraints excluded: chain E residue  286 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0980
   chunk 48 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 77 optimal weight:    9.9990
   chunk 69 optimal weight:   10.0000
   chunk 50 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 246 HIS
** B 130 ASN ** 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 = 0.3954 r_free = 0.3954 target = 0.153094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.131799 restraints weight = 10968.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.135165 restraints weight = 6307.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.137152 restraints weight = 4255.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7399  Z= 0.305
  Angle     :  0.645   7.825  10050  Z= 0.329
  Chirality :  0.047   0.154   1170
  Planarity :  0.004   0.033   1269
  Dihedral  :  5.489  29.712    972
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.55 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 16.07 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.27), residues: 880
  helix: -0.98 (1.03), residues: 19
  sheet: -1.12 (0.27), residues: 355
  loop : -2.31 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 290 
 HIS   0.003   0.001   HIS E 126 
 PHE   0.021   0.002   PHE D 247 
 TYR   0.021   0.002   TYR B 179 
 ARG   0.006   0.001   ARG B 276 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 116
  time to evaluate  : 0.819 
Fit side-chains
REVERT: A  163 ASN cc_start: 0.8651 (t0) cc_final: 0.8378 (t0)
REVERT: B  150 GLN cc_start: 0.8307 (mp-120) cc_final: 0.7968 (mt0)
REVERT: C  147 TYR cc_start: 0.5585 (t80) cc_final: 0.5144 (t80)
REVERT: E  257 TRP cc_start: 0.8839 (OUTLIER) cc_final: 0.8261 (t-100)
  outliers start: 35
  outliers final: 25
  residues processed: 142
  average time/residue: 0.1805
  time to fit residues: 34.7683
Evaluate side-chains
  137 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain B residue  147 TYR
Chi-restraints excluded: chain B residue  213 ASP
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain C residue  130 ASN
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain D residue  113 ASP
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  179 ASP
Chi-restraints excluded: chain D residue  190 VAL
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  250 ASP
Chi-restraints excluded: chain D residue  328 VAL
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  190 VAL
Chi-restraints excluded: chain E residue  257 TRP
Chi-restraints excluded: chain E residue  273 HIS
Chi-restraints excluded: chain E residue  286 THR
Chi-restraints excluded: chain E residue  305 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 46 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 59 optimal weight:    0.6980
   chunk 79 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 44 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.156981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.136244 restraints weight = 10802.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.139561 restraints weight = 6202.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.141666 restraints weight = 4185.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7399  Z= 0.177
  Angle     :  0.583   7.396  10050  Z= 0.296
  Chirality :  0.045   0.158   1170
  Planarity :  0.003   0.030   1269
  Dihedral  :  5.113  25.193    972
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 18.77 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.28), residues: 880
  helix: -1.24 (0.95), residues: 19
  sheet: -1.08 (0.27), residues: 358
  loop : -2.15 (0.27), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP E 257 
 HIS   0.002   0.001   HIS E 126 
 PHE   0.017   0.001   PHE D 247 
 TYR   0.017   0.001   TYR B 179 
 ARG   0.007   0.001   ARG E 243 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
REVERT: A  162 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7775 (mtpp)
REVERT: A  163 ASN cc_start: 0.8536 (t0) cc_final: 0.8282 (t0)
REVERT: B  150 GLN cc_start: 0.8303 (mp-120) cc_final: 0.7948 (mt0)
REVERT: C  147 TYR cc_start: 0.5298 (t80) cc_final: 0.4925 (t80)
REVERT: E  247 PHE cc_start: 0.8795 (t80) cc_final: 0.8581 (t80)
REVERT: E  257 TRP cc_start: 0.8744 (OUTLIER) cc_final: 0.8145 (t-100)
  outliers start: 24
  outliers final: 19
  residues processed: 135
  average time/residue: 0.1831
  time to fit residues: 33.8048
Evaluate side-chains
  127 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  179 ASP
Chi-restraints excluded: chain D residue  190 VAL
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  328 VAL
Chi-restraints excluded: chain D residue  330 VAL
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  255 ASP
Chi-restraints excluded: chain E residue  257 TRP
Chi-restraints excluded: chain E residue  286 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 62 optimal weight:    9.9990
   chunk 33 optimal weight:    0.1980
   chunk 29 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 78 optimal weight:    8.9990
   chunk 87 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    2.8388

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

Flipped N/Q/H residues before XYZ refinement:
** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.149911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.129877 restraints weight = 11009.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.132708 restraints weight = 6715.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.134515 restraints weight = 4331.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7399  Z= 0.348
  Angle     :  0.680   6.282  10050  Z= 0.348
  Chirality :  0.048   0.171   1170
  Planarity :  0.004   0.039   1269
  Dihedral  :  5.745  32.627    972
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 17.67 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.27), residues: 880
  helix: -0.82 (1.06), residues: 19
  sheet: -1.08 (0.28), residues: 332
  loop : -2.27 (0.26), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 290 
 HIS   0.006   0.001   HIS E 126 
 PHE   0.023   0.002   PHE D 247 
 TYR   0.020   0.002   TYR B 179 
 ARG   0.007   0.001   ARG B 276 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 109
  time to evaluate  : 0.901 
Fit side-chains
REVERT: B  150 GLN cc_start: 0.8236 (mp-120) cc_final: 0.7927 (mt0)
REVERT: E  247 PHE cc_start: 0.8764 (t80) cc_final: 0.8546 (t80)
REVERT: E  257 TRP cc_start: 0.8895 (OUTLIER) cc_final: 0.8417 (t-100)
  outliers start: 34
  outliers final: 29
  residues processed: 134
  average time/residue: 0.1819
  time to fit residues: 33.9985
Evaluate side-chains
  136 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 106
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain B residue  147 TYR
Chi-restraints excluded: chain B residue  213 ASP
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  179 ASP
Chi-restraints excluded: chain D residue  190 VAL
Chi-restraints excluded: chain D residue  220 ILE
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  250 ASP
Chi-restraints excluded: chain D residue  328 VAL
Chi-restraints excluded: chain D residue  330 VAL
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  255 ASP
Chi-restraints excluded: chain E residue  257 TRP
Chi-restraints excluded: chain E residue  273 HIS
Chi-restraints excluded: chain E residue  274 ILE
Chi-restraints excluded: chain E residue  286 THR
Chi-restraints excluded: chain E residue  305 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 54 optimal weight:    9.9990
   chunk 46 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0050
   chunk 39 optimal weight:    6.9990
   chunk 58 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9990
   chunk 88 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    2.2002

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

Flipped N/Q/H residues before XYZ refinement:
** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.151796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.130925 restraints weight = 10986.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.134208 restraints weight = 6188.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.136218 restraints weight = 4152.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7399  Z= 0.279
  Angle     :  0.642   7.869  10050  Z= 0.327
  Chirality :  0.047   0.152   1170
  Planarity :  0.004   0.032   1269
  Dihedral  :  5.562  29.047    972
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 17.18 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.27), residues: 880
  helix: -0.89 (1.07), residues: 19
  sheet: -1.17 (0.28), residues: 344
  loop : -2.14 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 134 
 HIS   0.004   0.001   HIS A 246 
 PHE   0.019   0.002   PHE D 247 
 TYR   0.022   0.002   TYR B 179 
 ARG   0.008   0.001   ARG E 243 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 103
  time to evaluate  : 0.933 
Fit side-chains
REVERT: A  162 LYS cc_start: 0.8257 (mtmm) cc_final: 0.7941 (mtpp)
REVERT: A  163 ASN cc_start: 0.8670 (t0) cc_final: 0.8400 (t0)
REVERT: B  150 GLN cc_start: 0.8245 (mp-120) cc_final: 0.7907 (mt0)
REVERT: D  183 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.6623 (m-70)
REVERT: E  257 TRP cc_start: 0.8864 (OUTLIER) cc_final: 0.8329 (t-100)
  outliers start: 37
  outliers final: 33
  residues processed: 129
  average time/residue: 0.1721
  time to fit residues: 31.3041
Evaluate side-chains
  136 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 101
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain B residue  147 TYR
Chi-restraints excluded: chain B residue  206 ASP
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain C residue  172 THR
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  179 ASP
Chi-restraints excluded: chain D residue  183 HIS
Chi-restraints excluded: chain D residue  190 VAL
Chi-restraints excluded: chain D residue  220 ILE
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  250 ASP
Chi-restraints excluded: chain D residue  328 VAL
Chi-restraints excluded: chain D residue  330 VAL
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  190 VAL
Chi-restraints excluded: chain E residue  241 VAL
Chi-restraints excluded: chain E residue  255 ASP
Chi-restraints excluded: chain E residue  257 TRP
Chi-restraints excluded: chain E residue  273 HIS
Chi-restraints excluded: chain E residue  286 THR
Chi-restraints excluded: chain E residue  305 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 54 optimal weight:    9.9990
   chunk 30 optimal weight:    3.9990
   chunk 39 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0060
   chunk 2 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 83 optimal weight:    8.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    2.0004

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

Flipped N/Q/H residues before XYZ refinement:
** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.152433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.132178 restraints weight = 10922.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.135476 restraints weight = 6442.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.137862 restraints weight = 3984.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7399  Z= 0.262
  Angle     :  0.635   7.293  10050  Z= 0.323
  Chirality :  0.047   0.165   1170
  Planarity :  0.004   0.032   1269
  Dihedral  :  5.487  28.530    972
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 17.55 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.28), residues: 880
  helix: -0.78 (1.10), residues: 19
  sheet: -1.13 (0.28), residues: 344
  loop : -2.14 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 134 
 HIS   0.005   0.001   HIS A 246 
 PHE   0.020   0.002   PHE D 272 
 TYR   0.016   0.002   TYR A 170 
 ARG   0.008   0.001   ARG E 243 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 104
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
REVERT: A  162 LYS cc_start: 0.8269 (mtmm) cc_final: 0.7771 (mtpp)
REVERT: A  163 ASN cc_start: 0.8695 (t0) cc_final: 0.8418 (t0)
REVERT: B  150 GLN cc_start: 0.8237 (mp-120) cc_final: 0.7939 (mt0)
REVERT: C  213 ASP cc_start: 0.8293 (t0) cc_final: 0.8036 (t0)
REVERT: D  183 HIS cc_start: 0.7927 (OUTLIER) cc_final: 0.6587 (m-70)
REVERT: E  257 TRP cc_start: 0.8851 (OUTLIER) cc_final: 0.8286 (t-100)
  outliers start: 37
  outliers final: 34
  residues processed: 131
  average time/residue: 0.1704
  time to fit residues: 31.3119
Evaluate side-chains
  139 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 103
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain B residue  147 TYR
Chi-restraints excluded: chain B residue  206 ASP
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain C residue  172 THR
Chi-restraints excluded: chain C residue  215 GLU
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  313 SER
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  179 ASP
Chi-restraints excluded: chain D residue  183 HIS
Chi-restraints excluded: chain D residue  190 VAL
Chi-restraints excluded: chain D residue  220 ILE
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  250 ASP
Chi-restraints excluded: chain D residue  328 VAL
Chi-restraints excluded: chain D residue  330 VAL
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  190 VAL
Chi-restraints excluded: chain E residue  241 VAL
Chi-restraints excluded: chain E residue  255 ASP
Chi-restraints excluded: chain E residue  257 TRP
Chi-restraints excluded: chain E residue  273 HIS
Chi-restraints excluded: chain E residue  286 THR
Chi-restraints excluded: chain E residue  305 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 63 optimal weight:   10.0000
   chunk 70 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 246 HIS
** B 130 ASN ** 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 = 0.3982 r_free = 0.3982 target = 0.154904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.134871 restraints weight = 11109.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.137922 restraints weight = 6692.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.140635 restraints weight = 4234.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.3133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7399  Z= 0.205
  Angle     :  0.622  11.592  10050  Z= 0.312
  Chirality :  0.046   0.162   1170
  Planarity :  0.004   0.032   1269
  Dihedral  :  5.300  26.942    972
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 18.40 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.28), residues: 880
  helix: -0.92 (1.08), residues: 19
  sheet: -1.03 (0.27), residues: 363
  loop : -2.08 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 134 
 HIS   0.006   0.001   HIS A 246 
 PHE   0.018   0.001   PHE D 247 
 TYR   0.023   0.001   TYR B 179 
 ARG   0.007   0.001   ARG E 243 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 104
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: A  162 LYS cc_start: 0.8205 (mtmm) cc_final: 0.7666 (mtpp)
REVERT: A  163 ASN cc_start: 0.8645 (t0) cc_final: 0.8382 (t0)
REVERT: A  246 HIS cc_start: 0.6105 (OUTLIER) cc_final: 0.5493 (m90)
REVERT: B  150 GLN cc_start: 0.8241 (mp-120) cc_final: 0.7931 (mt0)
REVERT: C  213 ASP cc_start: 0.8282 (t0) cc_final: 0.8028 (t0)
REVERT: D  183 HIS cc_start: 0.7993 (OUTLIER) cc_final: 0.6733 (m-70)
REVERT: E  257 TRP cc_start: 0.8837 (OUTLIER) cc_final: 0.8301 (t-100)
  outliers start: 33
  outliers final: 29
  residues processed: 128
  average time/residue: 0.1686
  time to fit residues: 30.3099
Evaluate side-chains
  134 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 102
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  246 HIS
Chi-restraints excluded: chain B residue  147 TYR
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain C residue  172 THR
Chi-restraints excluded: chain C residue  215 GLU
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  313 SER
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  179 ASP
Chi-restraints excluded: chain D residue  183 HIS
Chi-restraints excluded: chain D residue  190 VAL
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  250 ASP
Chi-restraints excluded: chain D residue  328 VAL
Chi-restraints excluded: chain D residue  330 VAL
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  190 VAL
Chi-restraints excluded: chain E residue  241 VAL
Chi-restraints excluded: chain E residue  255 ASP
Chi-restraints excluded: chain E residue  257 TRP
Chi-restraints excluded: chain E residue  286 THR
Chi-restraints excluded: chain E residue  305 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 83 optimal weight:    8.9990
   chunk 44 optimal weight:    0.2980
   chunk 9 optimal weight:    0.2980
   chunk 52 optimal weight:    8.9990
   chunk 63 optimal weight:    8.9990
   chunk 64 optimal weight:    0.6980
   chunk 18 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 246 HIS
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 ASN
C 130 ASN
E 126 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.158439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.139477 restraints weight = 10740.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.142036 restraints weight = 6945.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.143890 restraints weight = 4587.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7399  Z= 0.159
  Angle     :  0.590   7.553  10050  Z= 0.298
  Chirality :  0.045   0.148   1170
  Planarity :  0.004   0.032   1269
  Dihedral  :  4.931  25.396    972
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 19.14 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.28), residues: 880
  helix: -1.84 (0.85), residues: 25
  sheet: -0.88 (0.27), residues: 362
  loop : -2.03 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 134 
 HIS   0.006   0.001   HIS A 246 
 PHE   0.018   0.001   PHE D 247 
 TYR   0.018   0.001   TYR B 179 
 ARG   0.007   0.001   ARG E 243 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2156.15 seconds
wall clock time: 40 minutes 3.49 seconds (2403.49 seconds total)