Starting phenix.real_space_refine
on Sun Apr 27 12:45:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qnt_4608/04_2025/6qnt_4608.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qnt_4608/04_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_4608/04_2025/6qnt_4608.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qnt_4608/04_2025/6qnt_4608.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qnt_4608/04_2025/6qnt_4608.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qnt_4608/04_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-5669/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: 3.80, 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: 1.13
  Conformation dependent library (CDL) restraints added in 662.9 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: 0.65
  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: 1.40

  Time building geometry restraints manager: 1.39 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:             0.510
  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:                    0.050
  Process input model:                     16.380
  Find NCS groups from input model:        0.180
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.430
-------------------------------------------------------------------------------
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= 0.206
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.28418 (  132)
  hydrogen bonds       : angle      10.56961 (  387)
  covalent geometry    : bond        0.00427 ( 5899)
  covalent geometry    : angle       0.85169 ( 8018)

*********************** 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  : 0.597 
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: 0.2089
  time to fit residues: 39.2592
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  : 0.604 
-------------------------------------------------------------------------------
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 = 32)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.107226 restraints weight = 8110.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.110721 restraints weight = 4279.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.113090 restraints weight = 2737.939|
|-----------------------------------------------------------------------------|
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= 0.181
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04053 (  132)
  hydrogen bonds       : angle       6.55094 (  387)
  covalent geometry    : bond        0.00426 ( 5899)
  covalent geometry    : angle       0.62961 ( 8018)

*********************** 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  : 0.577 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 ASN cc_start: 0.5416 (p0) cc_final: 0.5059 (p0)
REVERT: A  246 HIS cc_start: 0.8023 (m-70) cc_final: 0.7747 (m-70)
REVERT: B  256 TYR cc_start: 0.8946 (m-80) cc_final: 0.8370 (m-80)
REVERT: B  315 ILE cc_start: 0.9094 (mt) cc_final: 0.8841 (mt)
REVERT: C  272 MET cc_start: 0.7977 (tmm) cc_final: 0.7073 (tmm)
REVERT: D  282 GLU cc_start: 0.8060 (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: 0.8509 (ttmm)
  outliers start: 8
  outliers final: 6
  residues processed: 109
  average time/residue: 0.1914
  time to fit residues: 26.8434
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  : 0.599 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 63 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.6760

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.128758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.110679 restraints weight = 8016.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.114348 restraints weight = 4177.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.116780 restraints weight = 2643.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   5899  Z= 0.101
  Angle     :  0.551   7.199   8018  Z= 0.280
  Chirality :  0.043   0.134    927
  Planarity :  0.003   0.031   1013
  Dihedral  :  5.137  34.440    778
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  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 : 0.29 %

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: -3.14 (0.28), residues: 705
  helix: -3.89 (0.29), residues: 32
  sheet: -1.33 (0.30), residues: 284
  loop : -2.56 (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   0.019   0.001   PHE D 247 
 TYR   0.012   0.001   TYR A 256 
 ARG   0.005   0.000   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03125 (  132)
  hydrogen bonds       : angle       5.88499 (  387)
  covalent geometry    : bond        0.00233 ( 5899)
  covalent geometry    : angle       0.55095 ( 8018)

*********************** 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  : 0.590 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 LYS cc_start: 0.8517 (tmtt) cc_final: 0.8270 (tptp)
REVERT: A  246 HIS cc_start: 0.7955 (m-70) cc_final: 0.7706 (m-70)
REVERT: B  134 TRP cc_start: 0.8360 (m100) cc_final: 0.7778 (m100)
REVERT: B  256 TYR cc_start: 0.8921 (m-80) cc_final: 0.8263 (m-80)
REVERT: B  315 ILE cc_start: 0.9015 (mt) cc_final: 0.8766 (mt)
REVERT: C  272 MET cc_start: 0.7766 (tmm) cc_final: 0.6826 (tmm)
REVERT: D  282 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7756 (mt-10)
REVERT: D  320 LYS cc_start: 0.8818 (mttm) cc_final: 0.8570 (ttmm)
  outliers start: 9
  outliers final: 5
  residues processed: 113
  average time/residue: 0.1951
  time to fit residues: 28.1244
Evaluate side-chains
  102 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0770
   chunk 19 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 64 optimal weight:    0.8980
   chunk 8 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    1.5542

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.125465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.107279 restraints weight = 8282.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.110900 restraints weight = 4340.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.113210 restraints weight = 2765.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5899  Z= 0.160
  Angle     :  0.588   7.369   8018  Z= 0.297
  Chirality :  0.044   0.134    927
  Planarity :  0.004   0.030   1013
  Dihedral  :  5.211  34.777    778
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.33 %
    Favored  : 81.66 %
  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: -2.93 (0.28), residues: 705
  helix: -3.71 (0.34), residues: 32
  sheet: -1.21 (0.30), residues: 284
  loop : -2.40 (0.27), residues: 389

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   0.023   0.001   PHE D 247 
 TYR   0.010   0.001   TYR B 170 
 ARG   0.003   0.000   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03263 (  132)
  hydrogen bonds       : angle       5.71335 (  387)
  covalent geometry    : bond        0.00378 ( 5899)
  covalent geometry    : angle       0.58783 ( 8018)

*********************** 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
  115 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 LYS cc_start: 0.8509 (tmtt) cc_final: 0.8146 (tmtt)
REVERT: A  246 HIS cc_start: 0.8131 (m-70) cc_final: 0.7925 (m-70)
REVERT: B  134 TRP cc_start: 0.8480 (m100) cc_final: 0.7815 (m100)
REVERT: B  256 TYR cc_start: 0.8978 (m-80) cc_final: 0.8370 (m-80)
REVERT: B  315 ILE cc_start: 0.9038 (mt) cc_final: 0.8774 (mt)
REVERT: C  272 MET cc_start: 0.7833 (tmm) cc_final: 0.6920 (tmm)
REVERT: D  188 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7288 (pp)
REVERT: D  277 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7858 (m-30)
REVERT: D  282 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7777 (mt-10)
  outliers start: 13
  outliers final: 10
  residues processed: 111
  average time/residue: 0.1872
  time to fit residues: 26.6301
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  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 TYR
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  274 ILE
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  284 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 64 optimal weight:    6.9990
   chunk 50 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0470
   chunk 8 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.9082

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.128365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.109992 restraints weight = 8051.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.113611 restraints weight = 4249.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.116059 restraints weight = 2721.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
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= 0.114
  Angle     :  0.551   7.165   8018  Z= 0.278
  Chirality :  0.043   0.132    927
  Planarity :  0.003   0.030   1013
  Dihedral  :  4.988  35.828    778
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 17.41 %
    Favored  : 80.89 %
  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: -2.71 (0.29), residues: 705
  helix: -3.53 (0.39), residues: 32
  sheet: -1.06 (0.31), residues: 284
  loop : -2.26 (0.27), residues: 389

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   0.020   0.001   PHE D 247 
 TYR   0.009   0.001   TYR D 319 
 ARG   0.009   0.001   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02892 (  132)
  hydrogen bonds       : angle       5.50646 (  387)
  covalent geometry    : bond        0.00265 ( 5899)
  covalent geometry    : angle       0.55061 ( 8018)

*********************** 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
  113 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 LYS cc_start: 0.8433 (tmtt) cc_final: 0.8196 (tptp)
REVERT: B  134 TRP cc_start: 0.8305 (m100) cc_final: 0.7601 (m100)
REVERT: B  256 TYR cc_start: 0.8944 (m-80) cc_final: 0.8253 (m-80)
REVERT: B  315 ILE cc_start: 0.9000 (mt) cc_final: 0.8727 (mt)
REVERT: C  272 MET cc_start: 0.7748 (tmm) cc_final: 0.6839 (tmm)
REVERT: D  188 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7301 (pp)
REVERT: D  277 ASP cc_start: 0.8216 (t70) cc_final: 0.7858 (m-30)
REVERT: D  282 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7780 (mt-10)
  outliers start: 11
  outliers final: 7
  residues processed: 112
  average time/residue: 0.1966
  time to fit residues: 28.6831
Evaluate side-chains
  104 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  246 HIS
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  284 ILE
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:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 64 optimal weight:    0.4980
   chunk 47 optimal weight:    2.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    2.0584

-------------------------------------------------------------------------------
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**
C 246 HIS
D 206 GLN
D 298 ASN
** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.124321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.106145 restraints weight = 8145.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.109629 restraints weight = 4326.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.111962 restraints weight = 2797.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.2573

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= 0.199
  Angle     :  0.611   7.199   8018  Z= 0.314
  Chirality :  0.045   0.137    927
  Planarity :  0.004   0.030   1013
  Dihedral  :  5.365  36.909    778
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.22 %
    Favored  : 90.78 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 16.02 %
    Favored  : 80.59 %
  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: -2.71 (0.29), residues: 705
  helix: -3.41 (0.42), residues: 32
  sheet: -1.08 (0.31), residues: 284
  loop : -2.25 (0.27), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 134 
 HIS   0.007   0.001   HIS A 246 
 PHE   0.026   0.002   PHE D 247 
 TYR   0.013   0.001   TYR B 170 
 ARG   0.008   0.001   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03420 (  132)
  hydrogen bonds       : angle       5.60018 (  387)
  covalent geometry    : bond        0.00474 ( 5899)
  covalent geometry    : angle       0.61116 ( 8018)

*********************** 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  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ASN cc_start: 0.6425 (p0) cc_final: 0.6147 (p0)
REVERT: B  134 TRP cc_start: 0.8617 (m100) cc_final: 0.7728 (m100)
REVERT: B  218 TYR cc_start: 0.7323 (m-10) cc_final: 0.7087 (m-10)
REVERT: B  315 ILE cc_start: 0.9065 (mt) cc_final: 0.8773 (mt)
REVERT: C  272 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7018 (tmm)
REVERT: D  188 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7297 (pp)
REVERT: D  243 ARG cc_start: 0.7971 (mtt-85) cc_final: 0.7692 (mtp85)
REVERT: D  277 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7854 (m-30)
REVERT: D  282 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7823 (mt-10)
  outliers start: 22
  outliers final: 13
  residues processed: 114
  average time/residue: 0.1922
  time to fit residues: 28.0528
Evaluate side-chains
  115 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
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  212 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  272 MET
Chi-restraints excluded: chain C residue  286 MET
Chi-restraints excluded: chain D residue  116 VAL
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  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:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0020
   chunk 16 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0970
   chunk 18 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0270
   chunk 49 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.3644

-------------------------------------------------------------------------------
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**
** D 307 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 = 0.3554 r_free = 0.3554 target = 0.129876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.111709 restraints weight = 8051.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.115317 restraints weight = 4214.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.117849 restraints weight = 2696.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   5899  Z= 0.094
  Angle     :  0.539   7.346   8018  Z= 0.274
  Chirality :  0.043   0.133    927
  Planarity :  0.003   0.027   1013
  Dihedral  :  4.729  34.545    778
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.26 %
    Favored  : 80.59 %
  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: -2.39 (0.30), residues: 705
  helix: -2.97 (0.55), residues: 26
  sheet: -0.89 (0.32), residues: 284
  loop : -2.06 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 134 
 HIS   0.001   0.000   HIS B 246 
 PHE   0.019   0.001   PHE D 247 
 TYR   0.008   0.001   TYR D 319 
 ARG   0.008   0.001   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02604 (  132)
  hydrogen bonds       : angle       5.32597 (  387)
  covalent geometry    : bond        0.00217 ( 5899)
  covalent geometry    : angle       0.53907 ( 8018)

*********************** 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
  119 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 MET cc_start: 0.7663 (mmt) cc_final: 0.7232 (mmt)
REVERT: A  272 MET cc_start: 0.7668 (tmm) cc_final: 0.7370 (tmm)
REVERT: B  134 TRP cc_start: 0.8191 (m100) cc_final: 0.7522 (m100)
REVERT: B  256 TYR cc_start: 0.8882 (m-80) cc_final: 0.8227 (m-80)
REVERT: B  315 ILE cc_start: 0.8990 (mt) cc_final: 0.8722 (mt)
REVERT: C  272 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.6696 (tmm)
REVERT: D  188 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7284 (pp)
REVERT: D  243 ARG cc_start: 0.7899 (mtt-85) cc_final: 0.7624 (mtp85)
REVERT: D  277 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7849 (m-30)
REVERT: D  282 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7830 (mt-10)
  outliers start: 14
  outliers final: 8
  residues processed: 113
  average time/residue: 0.1916
  time to fit residues: 27.7921
Evaluate side-chains
  113 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  246 HIS
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  274 ILE
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:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0670
   chunk 23 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0060
   chunk 25 optimal weight:    0.7980
   chunk 52 optimal weight:    0.0570
   chunk 61 optimal weight:    6.9990
   overall best weight:    0.3052

-------------------------------------------------------------------------------
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
** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 307 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 = 0.3588 r_free = 0.3588 target = 0.132808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.114542 restraints weight = 7881.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.118321 restraints weight = 4074.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.120860 restraints weight = 2558.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   5899  Z= 0.087
  Angle     :  0.516   6.984   8018  Z= 0.263
  Chirality :  0.043   0.132    927
  Planarity :  0.003   0.028   1013
  Dihedral  :  4.353  33.115    778
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.57 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -2.19 (0.30), residues: 705
  helix: -2.84 (0.55), residues: 27
  sheet: -0.82 (0.31), residues: 294
  loop : -1.87 (0.29), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 134 
 HIS   0.001   0.000   HIS A 202 
 PHE   0.020   0.001   PHE D 247 
 TYR   0.007   0.001   TYR D 158 
 ARG   0.009   0.001   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02449 (  132)
  hydrogen bonds       : angle       5.07314 (  387)
  covalent geometry    : bond        0.00204 ( 5899)
  covalent geometry    : angle       0.51632 ( 8018)

*********************** 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
  126 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 LYS cc_start: 0.8468 (tmtt) cc_final: 0.8096 (tmtt)
REVERT: A  272 MET cc_start: 0.7424 (tmm) cc_final: 0.7124 (tmm)
REVERT: B  256 TYR cc_start: 0.8814 (m-80) cc_final: 0.8180 (m-80)
REVERT: B  276 ARG cc_start: 0.8223 (ttp-110) cc_final: 0.7839 (ptp90)
REVERT: B  315 ILE cc_start: 0.8968 (mt) cc_final: 0.8729 (mt)
REVERT: C  230 MET cc_start: 0.8438 (mmp) cc_final: 0.8113 (mmt)
REVERT: C  272 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6600 (tmm)
REVERT: C  273 LEU cc_start: 0.7480 (mt) cc_final: 0.7189 (mt)
REVERT: D  188 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7289 (pp)
REVERT: D  243 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7721 (mtp85)
REVERT: D  277 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7907 (m-30)
REVERT: D  282 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7849 (mt-10)
  outliers start: 13
  outliers final: 6
  residues processed: 120
  average time/residue: 0.2147
  time to fit residues: 33.1345
Evaluate side-chains
  113 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
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 C residue  206 ASP
Chi-restraints excluded: chain C residue  272 MET
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 59 optimal weight:    9.9990
   chunk 32 optimal weight:    5.9990
   chunk 15 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0670
   chunk 23 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.6920

-------------------------------------------------------------------------------
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
C 249 ASN
D 206 GLN
** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 307 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 = 0.3565 r_free = 0.3565 target = 0.130992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.112971 restraints weight = 7998.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.116603 restraints weight = 4195.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.119072 restraints weight = 2674.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   5899  Z= 0.102
  Angle     :  0.544   8.133   8018  Z= 0.275
  Chirality :  0.043   0.179    927
  Planarity :  0.003   0.034   1013
  Dihedral  :  4.479  35.930    778
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 18.64 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -2.10 (0.30), residues: 705
  helix: -2.83 (0.57), residues: 26
  sheet: -0.76 (0.32), residues: 285
  loop : -1.80 (0.28), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 134 
 HIS   0.001   0.000   HIS B 246 
 PHE   0.020   0.001   PHE D 247 
 TYR   0.007   0.001   TYR B 170 
 ARG   0.008   0.001   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02551 (  132)
  hydrogen bonds       : angle       5.07570 (  387)
  covalent geometry    : bond        0.00242 ( 5899)
  covalent geometry    : angle       0.54413 ( 8018)

*********************** 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
  120 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 LYS cc_start: 0.8421 (tmtt) cc_final: 0.8186 (tptt)
REVERT: A  246 HIS cc_start: 0.8173 (m90) cc_final: 0.7944 (m-70)
REVERT: A  272 MET cc_start: 0.7575 (tmm) cc_final: 0.7257 (tmm)
REVERT: B  256 TYR cc_start: 0.8819 (m-80) cc_final: 0.8164 (m-80)
REVERT: B  276 ARG cc_start: 0.8140 (ttp-110) cc_final: 0.7774 (ptp90)
REVERT: B  315 ILE cc_start: 0.8991 (mt) cc_final: 0.8739 (mt)
REVERT: C  182 THR cc_start: 0.8723 (t) cc_final: 0.8476 (t)
REVERT: C  272 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.6704 (tmm)
REVERT: D  188 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7317 (pp)
REVERT: D  243 ARG cc_start: 0.7943 (mtt-85) cc_final: 0.7699 (mtp85)
REVERT: D  277 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7898 (m-30)
REVERT: D  282 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7849 (mt-10)
  outliers start: 13
  outliers final: 7
  residues processed: 115
  average time/residue: 0.2559
  time to fit residues: 37.9335
Evaluate side-chains
  114 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
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  274 ASN
Chi-restraints excluded: chain C residue  206 ASP
Chi-restraints excluded: chain C residue  272 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0770
   chunk 27 optimal weight:    0.5980
   overall best weight:    1.9344

-------------------------------------------------------------------------------
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
** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 307 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 = 0.3581 r_free = 0.3581 target = 0.131250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.114787 restraints weight = 8005.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.117902 restraints weight = 4372.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.119920 restraints weight = 2863.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   5899  Z= 0.193
  Angle     :  0.627   7.196   8018  Z= 0.317
  Chirality :  0.046   0.167    927
  Planarity :  0.004   0.038   1013
  Dihedral  :  5.127  37.929    778
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 18.95 %
    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: -2.24 (0.30), residues: 705
  helix: -2.70 (0.60), residues: 26
  sheet: -0.87 (0.32), residues: 285
  loop : -1.91 (0.28), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 134 
 HIS   0.003   0.001   HIS D 273 
 PHE   0.020   0.002   PHE D 247 
 TYR   0.013   0.001   TYR D 319 
 ARG   0.009   0.001   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03167 (  132)
  hydrogen bonds       : angle       5.34015 (  387)
  covalent geometry    : bond        0.00467 ( 5899)
  covalent geometry    : angle       0.62729 ( 8018)

********************** 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
  119 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 ASN cc_start: 0.6656 (p0) cc_final: 0.6135 (p0)
REVERT: A  246 HIS cc_start: 0.7979 (m90) cc_final: 0.7726 (m-70)
REVERT: B  134 TRP cc_start: 0.8404 (m100) cc_final: 0.7889 (m100)
REVERT: B  256 TYR cc_start: 0.8872 (m-80) cc_final: 0.8454 (m-80)
REVERT: B  315 ILE cc_start: 0.9040 (mt) cc_final: 0.8754 (mt)
REVERT: C  230 MET cc_start: 0.7992 (mmp) cc_final: 0.7714 (mmt)
REVERT: C  272 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7134 (tmm)
REVERT: D  188 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7506 (pp)
REVERT: D  243 ARG cc_start: 0.7960 (mtt-85) cc_final: 0.7724 (mtp85)
REVERT: D  277 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7878 (m-30)
  outliers start: 12
  outliers final: 7
  residues processed: 114
  average time/residue: 0.2001
  time to fit residues: 29.1530
Evaluate side-chains
  112 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
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  212 THR
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain C residue  206 ASP
Chi-restraints excluded: chain C residue  272 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0570
   chunk 24 optimal weight:    0.4980
   chunk 4 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0770
   chunk 38 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.9260

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

Flipped N/Q/H residues before XYZ refinement:
A 130 ASN
** 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**
** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.134192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.117838 restraints weight = 7892.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.120985 restraints weight = 4282.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.123078 restraints weight = 2785.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.3058

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= 0.122
  Angle     :  0.598   9.236   8018  Z= 0.300
  Chirality :  0.044   0.174    927
  Planarity :  0.003   0.034   1013
  Dihedral  :  4.942  37.647    778
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 19.57 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -2.20 (0.30), residues: 705
  helix: -2.64 (0.63), residues: 26
  sheet: -0.89 (0.31), residues: 287
  loop : -1.83 (0.28), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 134 
 HIS   0.001   0.000   HIS D 273 
 PHE   0.020   0.001   PHE D 247 
 TYR   0.019   0.001   TYR C 236 
 ARG   0.009   0.001   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02736 (  132)
  hydrogen bonds       : angle       5.27435 (  387)
  covalent geometry    : bond        0.00292 ( 5899)
  covalent geometry    : angle       0.59842 ( 8018)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2124.96 seconds
wall clock time: 38 minutes 12.76 seconds (2292.76 seconds total)