Starting phenix.real_space_refine
on Tue Feb 11 12:56:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qnt_4608/02_2025/6qnt_4608.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qnt_4608/02_2025/6qnt_4608.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qnt_4608/02_2025/6qnt_4608.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qnt_4608/02_2025/6qnt_4608.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qnt_4608/02_2025/6qnt_4608.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qnt_4608/02_2025/6qnt_4608.cif"
  }
  resolution = 3.5
  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=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    3709      2.51       5
     N     928      2.21       5
     O    1117      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5774
  Number of models: 1
  Model: ""
    Number of chains: 4
    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
  Time building chain proxies: 3.79, per 1000 atoms: 0.66
  Number of scatterers: 5774
  At special positions: 0
  Unit cell: (93.896, 100.298, 91.762, 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      20     16.00
     O    1117      8.00
     N     928      7.00
     C    3709      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: 1.36
  Conformation dependent library (CDL) restraints added in 717.1 milliseconds
  

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1384

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 16 sheets defined
      3.3% alpha, 32.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 177 through 182
    Processing helix  chain 'A' and resid 246 through 248
      No H-bonds generated for 'chain 'A' and resid 246 through 248'
    Processing helix  chain 'B' and resid 182 through 186
      removed outlier: 3.524A  pdb=" N   ASN B 186 " --> pdb=" O   LEU B 183 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 182 through 186
      removed outlier: 3.671A  pdb=" N   LYS C 185 " --> pdb=" O   THR C 182 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASN C 186 " --> pdb=" O   LEU C 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 182 through 186'
    Processing helix  chain 'C' and resid 226 through 230
      removed outlier: 3.754A  pdb=" N   PHE C 229 " --> pdb=" O   ALA C 226 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 216
      removed outlier: 3.562A  pdb=" N   LEU A 160 " --> pdb=" O   LEU A 133 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 154 through 158
      removed outlier: 3.687A  pdb=" N   THR A 172 " --> pdb=" O   THR A 157 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 197
    Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 197
    Processing sheet with id=AA5, first strand: chain 'B' and resid 132 through 133
    Processing sheet with id=AA6, first strand: chain 'B' and resid 154 through 158
    Processing sheet with id=AA7, first strand: chain 'B' and resid 188 through 197
      removed outlier: 3.731A  pdb=" N   TYR B 284 " --> pdb=" O   PHE B 197 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU B 289 " --> pdb=" O   THR B 270 " (cutoff:3.500A)
      removed outlier: 5.524A  pdb=" N   ASN B 293 " --> pdb=" O   PRO B 266 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 215 through 216
      removed outlier: 3.990A  pdb=" N   VAL C 161 " --> pdb=" O   ASN C 168 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 154 through 158
    Processing sheet with id=AB1, first strand: chain 'C' and resid 188 through 189
      removed outlier: 3.653A  pdb=" N   LEU C 292 " --> pdb=" O   VAL C 189 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 188 through 189
      removed outlier: 3.653A  pdb=" N   LEU C 292 " --> pdb=" O   VAL C 189 " (cutoff:3.500A)
      removed outlier: 5.447A  pdb=" N   ASN C 293 " --> pdb=" O   PRO C 266 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 114 through 120
      removed outlier: 6.733A  pdb=" N   PHE D 115 " --> pdb=" O   GLN D 210 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   ARG D 212 " --> pdb=" O   PHE D 115 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   GLY D 117 " --> pdb=" O   ARG D 212 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   LEU D 214 " --> pdb=" O   GLY D 117 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   VAL D 119 " --> pdb=" O   LEU D 214 " (cutoff:3.500A)
      removed outlier: 7.407A  pdb=" N   THR D 187 " --> pdb=" O   LEU D 154 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   LEU D 154 " --> pdb=" O   THR D 187 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   THR D 189 " --> pdb=" O   VAL D 152 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 131
      removed outlier: 6.855A  pdb=" N   ILE D 171 " --> pdb=" O   VAL D 129 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 230 through 231
      removed outlier: 6.641A  pdb=" N   GLY D 230 " --> pdb=" O   LYS D 329 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'D' and resid 240 through 245
      removed outlier: 6.839A  pdb=" N   GLU D 240 " --> pdb=" O   LEU D 287 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   LEU D 287 " --> pdb=" O   GLU D 240 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   THR D 242 " --> pdb=" O   VAL D 285 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   VAL D 285 " --> pdb=" O   THR D 242 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLU D 282 " --> pdb=" O   ASP D 277 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 262 through 265
      removed outlier: 7.010A  pdb=" N   SER D 302 " --> pdb=" O   ALA D 264 " (cutoff:3.500A)

    149 hydrogen bonds defined for protein.
    387 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: 1.59

  Time building geometry restraints manager: 1.61 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: 1788
        1.34 -     1.46: 1082
        1.46 -     1.57: 2995
        1.57 -     1.69: 0
        1.69 -     1.80: 34
  Bond restraints: 5899
  Sorted by residual:
  bond pdb=" N   ASN A 274 "
       pdb=" CA  ASN A 274 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.030 1.29e-02 6.01e+03 5.53e+00
  bond pdb=" N   ASN B 274 "
       pdb=" CA  ASN B 274 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.29e-02 6.01e+03 4.57e+00
  bond pdb=" CA  LYS A 275 "
       pdb=" C   LYS A 275 "
    ideal  model  delta    sigma   weight residual
    1.523  1.547 -0.024 1.34e-02 5.57e+03 3.19e+00
  bond pdb=" CA  LYS C 275 "
       pdb=" C   LYS C 275 "
    ideal  model  delta    sigma   weight residual
    1.523  1.547 -0.024 1.34e-02 5.57e+03 3.16e+00
  bond pdb=" C   GLU D 155 "
       pdb=" N   PRO D 156 "
    ideal  model  delta    sigma   weight residual
    1.334  1.374 -0.040 2.34e-02 1.83e+03 2.95e+00
  ... (remaining 5894 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 7844
        2.43 -     4.85: 140
        4.85 -     7.28: 23
        7.28 -     9.70: 10
        9.70 -    12.13: 1
  Bond angle restraints: 8018
  Sorted by residual:
  angle pdb=" C   GLU D 234 "
        pdb=" N   ASN D 235 "
        pdb=" CA  ASN D 235 "
      ideal   model   delta    sigma   weight residual
     122.82  132.08   -9.26 1.42e+00 4.96e-01 4.25e+01
  angle pdb=" N   THR B 135 "
        pdb=" CA  THR B 135 "
        pdb=" C   THR B 135 "
      ideal   model   delta    sigma   weight residual
     113.89  106.62    7.27 1.58e+00 4.01e-01 2.12e+01
  angle pdb=" C   ASN A 274 "
        pdb=" N   LYS A 275 "
        pdb=" CA  LYS A 275 "
      ideal   model   delta    sigma   weight residual
     121.54  130.16   -8.62 1.91e+00 2.74e-01 2.03e+01
  angle pdb=" N   ASN D 235 "
        pdb=" CA  ASN D 235 "
        pdb=" C   ASN D 235 "
      ideal   model   delta    sigma   weight residual
     111.17  116.92   -5.75 1.41e+00 5.03e-01 1.66e+01
  angle pdb=" CA  TYR D 158 "
        pdb=" CB  TYR D 158 "
        pdb=" CG  TYR D 158 "
      ideal   model   delta    sigma   weight residual
     113.90  121.08   -7.18 1.80e+00 3.09e-01 1.59e+01
  ... (remaining 8013 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.52: 3116
       16.52 -    33.03: 316
       33.03 -    49.55: 65
       49.55 -    66.07: 9
       66.07 -    82.59: 5
  Dihedral angle restraints: 3511
    sinusoidal: 1368
      harmonic: 2143
  Sorted by residual:
  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 -132.74  -47.26     0      5.00e+00 4.00e-02 8.93e+01
  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 -136.92  -43.08     0      5.00e+00 4.00e-02 7.42e+01
  dihedral pdb=" CA  LEU C 273 "
           pdb=" C   LEU C 273 "
           pdb=" N   ASN C 274 "
           pdb=" CA  ASN C 274 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -139.58  -40.42     0      5.00e+00 4.00e-02 6.54e+01
  ... (remaining 3508 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 689
       0.053 -    0.107: 182
       0.107 -    0.160: 48
       0.160 -    0.213: 4
       0.213 -    0.267: 4
  Chirality restraints: 927
  Sorted by residual:
  chirality pdb=" CA  ASN D 235 "
            pdb=" N   ASN D 235 "
            pdb=" C   ASN D 235 "
            pdb=" CB  ASN D 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.78e+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    2.26    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CB  ILE B 145 "
            pdb=" CA  ILE B 145 "
            pdb=" CG1 ILE B 145 "
            pdb=" CG2 ILE B 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.88   -0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 924 not shown)

  Planarity restraints: 1013
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 275 "    0.013 2.00e-02 2.50e+03   2.60e-02 6.75e+00
        pdb=" C   LYS B 275 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   LYS B 275 "    0.017 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=" C   SER C 308 "    0.043 5.00e-02 4.00e+02   6.49e-02 6.73e+00
        pdb=" N   PRO C 309 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO C 309 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C 309 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 273 "   -0.012 2.00e-02 2.50e+03   2.48e-02 6.13e+00
        pdb=" C   LEU B 273 "    0.043 2.00e-02 2.50e+03
        pdb=" O   LEU B 273 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ASN B 274 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1010 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 1875
        2.84 -     3.36: 4172
        3.36 -     3.87: 9369
        3.87 -     4.39: 9650
        4.39 -     4.90: 18278
  Nonbonded interactions: 43344
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 257 "
            pdb=" OE2 GLU B 299 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   LEU B 204 "
            pdb=" OG  SER B 208 "
     model   vdw
     2.345 3.040
  nonbonded pdb=" OE1 GLU A 194 "
            pdb=" OH  TYR A 196 "
     model   vdw
     2.348 3.040
  nonbonded pdb=" O   VAL D 305 "
            pdb=" OH  TYR D 319 "
     model   vdw
     2.349 3.040
  nonbonded pdb=" O   LEU A 204 "
            pdb=" OG  SER A 208 "
     model   vdw
     2.366 3.040
  ... (remaining 43339 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))
}

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:             0.360
  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:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     16.800
  Find NCS groups from input model:        0.210
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
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   0.040   5899  Z= 0.279
  Angle     :  0.852  12.128   8018  Z= 0.460
  Chirality :  0.054   0.267    927
  Planarity :  0.007   0.065   1013
  Dihedral  : 13.952  82.587   2127
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.62 %
    Favored  : 95.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.73 %

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: -4.25 (0.25), residues: 705
  helix: -4.46 (0.22), residues: 32
  sheet: -2.09 (0.28), residues: 284
  loop : -3.34 (0.23), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 134 
 HIS   0.006   0.001   HIS B 246 
 PHE   0.016   0.002   PHE A 312 
 TYR   0.012   0.002   TYR A 314 
 ARG   0.002   0.000   ARG D 180 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
REVERT: A  246 HIS cc_start: 0.7775 (m-70) cc_final: 0.7574 (m-70)
REVERT: B  256 TYR cc_start: 0.8851 (m-80) cc_final: 0.8453 (m-80)
REVERT: B  315 ILE cc_start: 0.9085 (mt) cc_final: 0.8854 (mt)
REVERT: D  260 ASN cc_start: 0.8346 (t0) cc_final: 0.8102 (t0)
REVERT: D  282 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7622 (mt-10)
REVERT: D  320 LYS cc_start: 0.8706 (mttm) cc_final: 0.8381 (ttmm)
  outliers start: 1
  outliers final: 1
  residues processed: 151
  average time/residue: 0.2252
  time to fit residues: 42.3636
Evaluate side-chains
  111 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  176 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 18 optimal weight:    8.9990
   chunk 36 optimal weight:    7.9990
   chunk 28 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 168 ASN
A 188 ASN
** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 168 ASN
D 217 ASN
D 236 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.124945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.107188 restraints weight = 8109.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.110722 restraints weight = 4277.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.113089 restraints weight = 2734.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5899  Z= 0.283
  Angle     :  0.630   8.382   8018  Z= 0.323
  Chirality :  0.046   0.149    927
  Planarity :  0.005   0.038   1013
  Dihedral  :  5.716  36.249    778
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.38 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 12.63 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.73 %

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: -3.59 (0.27), residues: 705
  helix: -4.22 (0.26), residues: 31
  sheet: -1.66 (0.29), residues: 284
  loop : -2.86 (0.25), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 134 
 HIS   0.002   0.001   HIS D 183 
 PHE   0.023   0.002   PHE D 247 
 TYR   0.017   0.001   TYR A 256 
 ARG   0.008   0.001   ARG A 281 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 ASN cc_start: 0.5417 (p0) cc_final: 0.5060 (p0)
REVERT: A  246 HIS cc_start: 0.8023 (m-70) cc_final: 0.7747 (m-70)
REVERT: B  256 TYR cc_start: 0.8945 (m-80) cc_final: 0.8370 (m-80)
REVERT: B  315 ILE cc_start: 0.9093 (mt) cc_final: 0.8842 (mt)
REVERT: C  272 MET cc_start: 0.7976 (tmm) cc_final: 0.7072 (tmm)
REVERT: D  282 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7764 (mt-10)
REVERT: D  284 ILE cc_start: 0.7262 (mm) cc_final: 0.6999 (tt)
REVERT: D  320 LYS cc_start: 0.8757 (mttm) cc_final: 0.8508 (ttmm)
  outliers start: 8
  outliers final: 6
  residues processed: 109
  average time/residue: 0.1960
  time to fit residues: 27.2814
Evaluate side-chains
  102 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain C residue  146 GLU
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  190 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 50 optimal weight:    0.0870
   chunk 35 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 63 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0370
   chunk 48 optimal weight:    4.9990
   overall best weight:    1.0242

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

Flipped N/Q/H residues before XYZ refinement:
A 249 ASN
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 219 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.126796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.108832 restraints weight = 8071.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.112377 restraints weight = 4212.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.114806 restraints weight = 2689.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5899  Z= 0.193
  Angle     :  0.568   7.380   8018  Z= 0.289
  Chirality :  0.044   0.136    927
  Planarity :  0.004   0.031   1013
  Dihedral  :  5.277  35.114    778
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 14.18 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.44 %

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: -3.18 (0.28), residues: 705
  helix: -3.88 (0.29), residues: 32
  sheet: -1.36 (0.30), residues: 284
  loop : -2.60 (0.26), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 134 
 HIS   0.001   0.000   HIS B 246 
 PHE   0.020   0.001   PHE D 247 
 TYR   0.012   0.001   TYR A 256 
 ARG   0.005   0.000   ARG A 281 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 ASN cc_start: 0.5522 (p0) cc_final: 0.5030 (p0)
REVERT: A  149 LYS cc_start: 0.8515 (tmtt) cc_final: 0.8239 (tptp)
REVERT: A  246 HIS cc_start: 0.8019 (m-70) cc_final: 0.7787 (m-70)
REVERT: A  299 GLU cc_start: 0.8145 (pt0) cc_final: 0.7916 (pt0)
REVERT: B  134 TRP cc_start: 0.8463 (m100) cc_final: 0.7833 (m100)
REVERT: B  256 TYR cc_start: 0.8940 (m-80) cc_final: 0.8336 (m-80)
REVERT: B  315 ILE cc_start: 0.9045 (mt) cc_final: 0.8791 (mt)
REVERT: C  272 MET cc_start: 0.7843 (tmm) cc_final: 0.6917 (tmm)
REVERT: D  282 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7742 (mt-10)
REVERT: D  319 TYR cc_start: 0.8689 (t80) cc_final: 0.8467 (t80)
REVERT: D  320 LYS cc_start: 0.8825 (mttm) cc_final: 0.8576 (ttmm)
  outliers start: 9
  outliers final: 5
  residues processed: 113
  average time/residue: 0.2012
  time to fit residues: 28.9517
Evaluate side-chains
  105 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  277 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 39 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 19 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 64 optimal weight:    0.6980
   chunk 8 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   overall best weight:    2.2586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.123700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.105421 restraints weight = 8346.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.108966 restraints weight = 4406.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.111352 restraints weight = 2833.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5899  Z= 0.345
  Angle     :  0.635   9.039   8018  Z= 0.321
  Chirality :  0.046   0.138    927
  Planarity :  0.004   0.031   1013
  Dihedral  :  5.524  36.073    778
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 14.48 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.59 %

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: -3.02 (0.29), residues: 705
  helix: -3.79 (0.31), residues: 32
  sheet: -1.27 (0.31), residues: 284
  loop : -2.47 (0.27), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 134 
 HIS   0.002   0.001   HIS B 246 
 PHE   0.025   0.002   PHE D 247 
 TYR   0.012   0.001   TYR B 170 
 ARG   0.005   0.001   ARG A 281 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 LYS cc_start: 0.8554 (tmtt) cc_final: 0.8242 (tmtt)
REVERT: B  218 TYR cc_start: 0.7310 (m-10) cc_final: 0.7006 (m-10)
REVERT: B  256 TYR cc_start: 0.8998 (m-80) cc_final: 0.8408 (m-80)
REVERT: B  315 ILE cc_start: 0.9082 (mt) cc_final: 0.8788 (mt)
REVERT: C  272 MET cc_start: 0.7934 (tmm) cc_final: 0.7043 (tmm)
REVERT: D  188 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7341 (pp)
REVERT: D  277 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7860 (m-30)
REVERT: D  282 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7735 (mt-10)
REVERT: D  320 LYS cc_start: 0.8805 (mttm) cc_final: 0.8545 (ttmm)
  outliers start: 16
  outliers final: 10
  residues processed: 112
  average time/residue: 0.1952
  time to fit residues: 27.9722
Evaluate side-chains
  108 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain C residue  206 ASP
Chi-restraints excluded: chain C residue  286 MET
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  190 VAL
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  330 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 64 optimal weight:    7.9990
   chunk 50 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 8 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 246 HIS
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 298 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.125909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.107839 restraints weight = 8126.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.111413 restraints weight = 4294.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.113832 restraints weight = 2752.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5899  Z= 0.200
  Angle     :  0.565   7.506   8018  Z= 0.287
  Chirality :  0.044   0.136    927
  Planarity :  0.003   0.030   1013
  Dihedral  :  5.195  34.211    778
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 15.87 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -2.78 (0.29), residues: 705
  helix: -3.67 (0.34), residues: 32
  sheet: -1.12 (0.31), residues: 284
  loop : -2.29 (0.27), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 134 
 HIS   0.006   0.001   HIS A 246 
 PHE   0.022   0.001   PHE D 247 
 TYR   0.010   0.001   TYR A 256 
 ARG   0.009   0.001   ARG B 281 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 LYS cc_start: 0.8458 (tmtt) cc_final: 0.8206 (tptp)
REVERT: B  134 TRP cc_start: 0.8536 (m100) cc_final: 0.7912 (m100)
REVERT: B  218 TYR cc_start: 0.7211 (m-10) cc_final: 0.6938 (m-10)
REVERT: B  256 TYR cc_start: 0.8980 (m-80) cc_final: 0.8352 (m-80)
REVERT: B  315 ILE cc_start: 0.9009 (mt) cc_final: 0.8736 (mt)
REVERT: C  272 MET cc_start: 0.7801 (tmm) cc_final: 0.6892 (tmm)
REVERT: D  188 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7296 (pp)
REVERT: D  277 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7883 (m-30)
REVERT: D  320 LYS cc_start: 0.8782 (mttm) cc_final: 0.8544 (ttmm)
  outliers start: 17
  outliers final: 11
  residues processed: 118
  average time/residue: 0.2156
  time to fit residues: 32.0834
Evaluate side-chains
  111 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain C residue  206 ASP
Chi-restraints excluded: chain C residue  286 MET
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  274 ILE
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  330 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 37 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 246 HIS
D 206 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.122475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.104615 restraints weight = 8228.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.108072 restraints weight = 4366.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.110391 restraints weight = 2812.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   5899  Z= 0.338
  Angle     :  0.623   7.732   8018  Z= 0.320
  Chirality :  0.046   0.140    927
  Planarity :  0.004   0.029   1013
  Dihedral  :  5.517  36.176    778
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.08 %
    Favored  : 90.92 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 16.18 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.44 %

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: -2.73 (0.29), residues: 705
  helix: -3.31 (0.41), residues: 26
  sheet: -1.15 (0.31), residues: 284
  loop : -2.26 (0.27), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 134 
 HIS   0.002   0.001   HIS B 246 
 PHE   0.027   0.002   PHE D 247 
 TYR   0.015   0.002   TYR A 256 
 ARG   0.007   0.001   ARG B 281 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  218 TYR cc_start: 0.7385 (m-10) cc_final: 0.7126 (m-10)
REVERT: B  315 ILE cc_start: 0.9080 (mt) cc_final: 0.8794 (mt)
REVERT: C  213 ASP cc_start: 0.8173 (t0) cc_final: 0.7950 (t0)
REVERT: C  272 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7030 (tmm)
REVERT: D  188 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7260 (pp)
REVERT: D  277 ASP cc_start: 0.8317 (t70) cc_final: 0.7883 (m-30)
REVERT: D  282 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7818 (mt-10)
REVERT: D  320 LYS cc_start: 0.8825 (mttm) cc_final: 0.8559 (ttmm)
  outliers start: 22
  outliers final: 15
  residues processed: 115
  average time/residue: 0.2101
  time to fit residues: 30.5986
Evaluate side-chains
  113 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  248 GLU
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain C residue  206 ASP
Chi-restraints excluded: chain C residue  272 MET
Chi-restraints excluded: chain C residue  286 MET
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  190 VAL
Chi-restraints excluded: chain D residue  284 ILE
Chi-restraints excluded: chain D residue  330 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0170
   chunk 49 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.3824

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

Flipped N/Q/H residues before XYZ refinement:
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 206 GLN
D 208 GLN
** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.124292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.106404 restraints weight = 8216.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.109884 restraints weight = 4344.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.112300 restraints weight = 2786.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5899  Z= 0.236
  Angle     :  0.577   7.546   8018  Z= 0.296
  Chirality :  0.044   0.135    927
  Planarity :  0.003   0.028   1013
  Dihedral  :  5.265  36.468    778
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 15.87 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -2.55 (0.30), residues: 705
  helix: -2.86 (0.49), residues: 20
  sheet: -1.07 (0.32), residues: 284
  loop : -2.15 (0.28), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 134 
 HIS   0.002   0.000   HIS B 246 
 PHE   0.023   0.001   PHE D 247 
 TYR   0.011   0.001   TYR A 256 
 ARG   0.007   0.001   ARG A 281 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ASN cc_start: 0.6306 (p0) cc_final: 0.5903 (p0)
REVERT: A  230 MET cc_start: 0.7775 (mmt) cc_final: 0.7260 (mmt)
REVERT: B  218 TYR cc_start: 0.7375 (m-10) cc_final: 0.7122 (m-10)
REVERT: B  315 ILE cc_start: 0.9037 (mt) cc_final: 0.8756 (mt)
REVERT: C  272 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.6914 (tmm)
REVERT: D  188 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7282 (pp)
REVERT: D  277 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7831 (m-30)
REVERT: D  320 LYS cc_start: 0.8829 (mttm) cc_final: 0.8586 (ttmm)
  outliers start: 20
  outliers final: 13
  residues processed: 114
  average time/residue: 0.2152
  time to fit residues: 30.9762
Evaluate side-chains
  112 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain C residue  206 ASP
Chi-restraints excluded: chain C residue  272 MET
Chi-restraints excluded: chain C residue  286 MET
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  330 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0570
   chunk 61 optimal weight:    0.9990
   overall best weight:    1.4104

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

Flipped N/Q/H residues before XYZ refinement:
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 206 GLN
** D 217 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 = 0.3487 r_free = 0.3487 target = 0.124389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.106432 restraints weight = 8094.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.109897 restraints weight = 4288.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.112299 restraints weight = 2764.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5899  Z= 0.240
  Angle     :  0.583   7.094   8018  Z= 0.298
  Chirality :  0.045   0.136    927
  Planarity :  0.004   0.030   1013
  Dihedral  :  5.205  36.711    778
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.80 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 15.87 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -2.46 (0.30), residues: 705
  helix: -2.83 (0.50), residues: 20
  sheet: -1.01 (0.31), residues: 286
  loop : -2.09 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 134 
 HIS   0.002   0.001   HIS B 246 
 PHE   0.024   0.001   PHE D 247 
 TYR   0.010   0.001   TYR D 319 
 ARG   0.008   0.001   ARG A 281 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 ASN cc_start: 0.6413 (p0) cc_final: 0.5926 (p0)
REVERT: A  149 LYS cc_start: 0.8451 (tmtt) cc_final: 0.8018 (tmtt)
REVERT: A  230 MET cc_start: 0.7859 (mmt) cc_final: 0.7353 (mmt)
REVERT: B  218 TYR cc_start: 0.7426 (m-10) cc_final: 0.7148 (m-10)
REVERT: B  315 ILE cc_start: 0.9041 (mt) cc_final: 0.8755 (mt)
REVERT: C  162 LYS cc_start: 0.8866 (mtpt) cc_final: 0.8282 (mtmm)
REVERT: C  230 MET cc_start: 0.8593 (mmp) cc_final: 0.8250 (mmp)
REVERT: C  272 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.6916 (tmm)
REVERT: D  183 HIS cc_start: 0.6616 (OUTLIER) cc_final: 0.6275 (m-70)
REVERT: D  188 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7305 (pp)
REVERT: D  277 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7830 (m-30)
REVERT: D  320 LYS cc_start: 0.8801 (mttm) cc_final: 0.8536 (ttmm)
  outliers start: 24
  outliers final: 17
  residues processed: 116
  average time/residue: 0.2132
  time to fit residues: 31.1348
Evaluate side-chains
  118 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  248 GLU
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain C residue  206 ASP
Chi-restraints excluded: chain C residue  272 MET
Chi-restraints excluded: chain C residue  286 MET
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  183 HIS
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  190 VAL
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  284 ILE
Chi-restraints excluded: chain D residue  307 ASN
Chi-restraints excluded: chain D residue  330 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0470
   chunk 23 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0970
   chunk 42 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 188 ASN
D 206 GLN
** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.128620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.110504 restraints weight = 8023.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.114131 restraints weight = 4204.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.116561 restraints weight = 2680.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   5899  Z= 0.161
  Angle     :  0.549   6.486   8018  Z= 0.282
  Chirality :  0.044   0.132    927
  Planarity :  0.003   0.028   1013
  Dihedral  :  4.812  35.891    778
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.87 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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 (0.30), residues: 705
  helix: -2.68 (0.64), residues: 20
  sheet: -0.89 (0.32), residues: 286
  loop : -1.95 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 134 
 HIS   0.001   0.000   HIS B 246 
 PHE   0.022   0.001   PHE D 247 
 TYR   0.010   0.001   TYR D 319 
 ARG   0.007   0.001   ARG A 281 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 TYR cc_start: 0.7396 (t80) cc_final: 0.7156 (t80)
REVERT: A  149 LYS cc_start: 0.8456 (tmtt) cc_final: 0.8050 (tmtt)
REVERT: A  230 MET cc_start: 0.7768 (mmt) cc_final: 0.7231 (mmt)
REVERT: B  134 TRP cc_start: 0.8350 (m100) cc_final: 0.7620 (m100)
REVERT: B  218 TYR cc_start: 0.7182 (m-10) cc_final: 0.6871 (m-10)
REVERT: B  256 TYR cc_start: 0.8900 (m-80) cc_final: 0.8264 (m-80)
REVERT: B  276 ARG cc_start: 0.8255 (ttp-110) cc_final: 0.8050 (ptp90)
REVERT: B  315 ILE cc_start: 0.8997 (mt) cc_final: 0.8729 (mt)
REVERT: C  162 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8173 (mtmm)
REVERT: C  272 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.6713 (tmm)
REVERT: D  188 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7253 (pp)
REVERT: D  277 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7818 (m-30)
REVERT: D  282 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7424 (tt0)
  outliers start: 16
  outliers final: 8
  residues processed: 122
  average time/residue: 0.1901
  time to fit residues: 29.4818
Evaluate side-chains
  114 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain C residue  188 ASN
Chi-restraints excluded: chain C residue  272 MET
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  307 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 10 optimal weight:    0.4980
   chunk 69 optimal weight:    6.9990
   chunk 60 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 188 ASN
C 246 HIS
D 206 GLN
** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.125481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.107186 restraints weight = 8208.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.110723 restraints weight = 4357.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.113012 restraints weight = 2809.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5899  Z= 0.248
  Angle     :  0.590   6.570   8018  Z= 0.303
  Chirality :  0.045   0.131    927
  Planarity :  0.004   0.033   1013
  Dihedral  :  5.066  38.071    778
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 18.49 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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 (0.30), residues: 705
  helix: -2.58 (0.65), residues: 20
  sheet: -0.90 (0.32), residues: 286
  loop : -1.96 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 134 
 HIS   0.002   0.001   HIS B 246 
 PHE   0.022   0.001   PHE D 247 
 TYR   0.012   0.001   TYR D 319 
 ARG   0.007   0.001   ARG A 281 

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 ASN cc_start: 0.6703 (p0) cc_final: 0.6273 (p0)
REVERT: A  149 LYS cc_start: 0.8458 (tmtt) cc_final: 0.8035 (tmtt)
REVERT: A  272 MET cc_start: 0.7780 (tmm) cc_final: 0.7555 (tmm)
REVERT: B  134 TRP cc_start: 0.8526 (m100) cc_final: 0.7805 (m100)
REVERT: B  218 TYR cc_start: 0.7235 (m-10) cc_final: 0.6911 (m-10)
REVERT: B  256 TYR cc_start: 0.8943 (m-80) cc_final: 0.8283 (m-80)
REVERT: B  276 ARG cc_start: 0.8093 (ttp-110) cc_final: 0.7877 (ptp90)
REVERT: B  315 ILE cc_start: 0.9039 (mt) cc_final: 0.8769 (mt)
REVERT: C  272 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.6885 (tmm)
REVERT: D  188 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7263 (pp)
REVERT: D  277 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7776 (m-30)
REVERT: D  282 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7547 (tt0)
  outliers start: 15
  outliers final: 10
  residues processed: 108
  average time/residue: 0.1876
  time to fit residues: 26.3033
Evaluate side-chains
  112 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  248 GLU
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain C residue  206 ASP
Chi-restraints excluded: chain C residue  272 MET
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  208 GLN
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  307 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 25 optimal weight:    0.3980
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 188 ASN
C 246 HIS
D 206 GLN
** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.127043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.108896 restraints weight = 8136.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.112439 restraints weight = 4286.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.114820 restraints weight = 2752.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5899  Z= 0.199
  Angle     :  0.566   6.383   8018  Z= 0.291
  Chirality :  0.044   0.130    927
  Planarity :  0.003   0.027   1013
  Dihedral  :  4.942  37.981    778
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 18.95 %
    Favored  : 78.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -2.21 (0.30), residues: 705
  helix: -2.40 (0.68), residues: 20
  sheet: -0.83 (0.32), residues: 286
  loop : -1.93 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 134 
 HIS   0.002   0.000   HIS B 246 
 PHE   0.021   0.001   PHE D 247 
 TYR   0.012   0.001   TYR D 319 
 ARG   0.007   0.001   ARG A 281 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1929.84 seconds
wall clock time: 35 minutes 18.22 seconds (2118.22 seconds total)