Starting phenix.real_space_refine
on Tue Mar  3 14:00:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qnt_4608/03_2026/6qnt_4608.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qnt_4608/03_2026/6qnt_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qnt_4608/03_2026/6qnt_4608.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qnt_4608/03_2026/6qnt_4608.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qnt_4608/03_2026/6qnt_4608.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qnt_4608/03_2026/6qnt_4608.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.88, per 1000 atoms: 0.33
  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: 0.44
  Conformation dependent library (CDL) restraints added in 342.9 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: 0.12
  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: 0.69

  Time building geometry restraints manager: 0.62 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:             0.610
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.200
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.210
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.002   0.000   ARG D 180 
 TYR   0.012   0.002   TYR A 314 
 PHE   0.016   0.002   PHE A 312 
 TRP   0.015   0.002   TRP C 134 
 HIS   0.006   0.001   HIS B 246 

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

*********************** 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  : 0.134 
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: 0.8452 (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: 0.0905
  time to fit residues: 17.1228
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  : 0.218 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0000
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0870
   overall best weight:    0.9766

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

Flipped N/Q/H residues before XYZ refinement:
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 219 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 = 0.3520 r_free = 0.3520 target = 0.126605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.108775 restraints weight = 8090.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.112392 restraints weight = 4215.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.114756 restraints weight = 2668.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.116397 restraints weight = 1915.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.117463 restraints weight = 1480.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5899  Z= 0.125
  Angle     :  0.591   8.318   8018  Z= 0.302
  Chirality :  0.044   0.148    927
  Planarity :  0.004   0.036   1013
  Dihedral  :  5.459  34.947    778
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 12.63 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.59 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.55 (0.27), residues: 705
  helix: -4.07 (0.29), residues: 31
  sheet: -1.62 (0.29), residues: 284
  loop : -2.85 (0.25), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 281 
 TYR   0.015   0.001   TYR A 256 
 PHE   0.021   0.001   PHE D 247 
 TRP   0.018   0.002   TRP C 134 
 HIS   0.001   0.000   HIS D 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 5899)
  covalent geometry    : angle       0.59127 ( 8018)
  hydrogen bonds       : bond        0.03902 (  132)
  hydrogen bonds       : angle       6.56168 (  387)

*********************** 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
  117 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 110
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 ASN cc_start: 0.5441 (p0) cc_final: 0.5089 (p0)
REVERT: A  246 HIS cc_start: 0.7912 (m-70) cc_final: 0.7641 (m-70)
REVERT: B  134 TRP cc_start: 0.8497 (m100) cc_final: 0.7927 (m100)
REVERT: B  256 TYR cc_start: 0.8910 (m-80) cc_final: 0.8283 (m-80)
REVERT: B  315 ILE cc_start: 0.9091 (mt) cc_final: 0.8862 (mt)
REVERT: D  210 GLN cc_start: 0.7547 (tt0) cc_final: 0.7327 (tp40)
REVERT: D  282 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7748 (mt-10)
REVERT: D  284 ILE cc_start: 0.7191 (mm) cc_final: 0.6955 (tt)
REVERT: D  320 LYS cc_start: 0.8740 (mttm) cc_final: 0.8492 (ttmm)
  outliers start: 7
  outliers final: 4
  residues processed: 114
  average time/residue: 0.0801
  time to fit residues: 11.7890
Evaluate side-chains
  103 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
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  151 ASN
Chi-restraints excluded: chain D residue  176 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 42 optimal weight:    6.9990
   chunk 29 optimal weight:    0.3980
   chunk 6 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0870
   chunk 48 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    1.6962

-------------------------------------------------------------------------------
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 = 0.3489 r_free = 0.3489 target = 0.124527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.106502 restraints weight = 8191.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.109954 restraints weight = 4338.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.112318 restraints weight = 2788.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.113900 restraints weight = 2015.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.114928 restraints weight = 1577.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.2130

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= 0.173
  Angle     :  0.604   7.758   8018  Z= 0.308
  Chirality :  0.045   0.136    927
  Planarity :  0.004   0.031   1013
  Dihedral  :  5.490  38.619    778
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 14.33 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.59 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.18 (0.28), residues: 705
  helix: -3.87 (0.29), residues: 33
  sheet: -1.35 (0.30), residues: 284
  loop : -2.60 (0.26), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 281 
 TYR   0.012   0.001   TYR B 170 
 PHE   0.023   0.001   PHE D 247 
 TRP   0.020   0.002   TRP C 134 
 HIS   0.002   0.001   HIS D 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 5899)
  covalent geometry    : angle       0.60361 ( 8018)
  hydrogen bonds       : bond        0.03651 (  132)
  hydrogen bonds       : angle       5.97765 (  387)

*********************** 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
  115 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ASN cc_start: 0.5663 (p0) cc_final: 0.5129 (p0)
REVERT: A  149 LYS cc_start: 0.8523 (tmtt) cc_final: 0.8298 (tptp)
REVERT: B  134 TRP cc_start: 0.8552 (m100) cc_final: 0.7906 (m100)
REVERT: B  256 TYR cc_start: 0.8981 (m-80) cc_final: 0.8403 (m-80)
REVERT: B  315 ILE cc_start: 0.9063 (mt) cc_final: 0.8796 (mt)
REVERT: D  282 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7723 (mt-10)
REVERT: D  320 LYS cc_start: 0.8850 (mttm) cc_final: 0.8601 (ttmm)
  outliers start: 9
  outliers final: 6
  residues processed: 111
  average time/residue: 0.0842
  time to fit residues: 11.9340
Evaluate side-chains
  105 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
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  190 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 16 optimal weight:    0.9990
   chunk 57 optimal weight:    8.9990
   chunk 51 optimal weight:    7.9990
   chunk 56 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 61 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 219 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.126415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.108317 restraints weight = 8104.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.111911 restraints weight = 4254.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.114243 restraints weight = 2720.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.115875 restraints weight = 1973.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.116954 restraints weight = 1539.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5899  Z= 0.140
  Angle     :  0.569   7.515   8018  Z= 0.288
  Chirality :  0.044   0.134    927
  Planarity :  0.003   0.029   1013
  Dihedral  :  5.217  37.501    778
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.72 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.91 (0.29), residues: 705
  helix: -3.69 (0.36), residues: 32
  sheet: -1.19 (0.31), residues: 284
  loop : -2.39 (0.27), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 276 
 TYR   0.009   0.001   TYR B 170 
 PHE   0.022   0.001   PHE D 247 
 TRP   0.020   0.002   TRP C 134 
 HIS   0.005   0.001   HIS A 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 5899)
  covalent geometry    : angle       0.56881 ( 8018)
  hydrogen bonds       : bond        0.03138 (  132)
  hydrogen bonds       : angle       5.70135 (  387)

*********************** 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
  120 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 LYS cc_start: 0.8426 (tmtt) cc_final: 0.8202 (tptp)
REVERT: A  246 HIS cc_start: 0.8043 (m90) cc_final: 0.7816 (m-70)
REVERT: B  134 TRP cc_start: 0.8473 (m100) cc_final: 0.7773 (m100)
REVERT: B  218 TYR cc_start: 0.7258 (m-10) cc_final: 0.6950 (m-10)
REVERT: B  256 TYR cc_start: 0.8972 (m-80) cc_final: 0.8285 (m-80)
REVERT: B  315 ILE cc_start: 0.9018 (mt) cc_final: 0.8730 (mt)
REVERT: D  188 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7320 (pp)
REVERT: D  277 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7856 (m-30)
REVERT: D  282 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7774 (mt-10)
REVERT: D  320 LYS cc_start: 0.8817 (mttm) cc_final: 0.8554 (ttmm)
  outliers start: 15
  outliers final: 9
  residues processed: 114
  average time/residue: 0.0836
  time to fit residues: 12.2935
Evaluate side-chains
  109 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    8.9990
   chunk 69 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 63 optimal weight:    6.9990
   chunk 6 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 168 ASN
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 246 HIS
D 298 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.120760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.102681 restraints weight = 8454.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.106163 restraints weight = 4453.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.108487 restraints weight = 2871.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.110037 restraints weight = 2087.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.111107 restraints weight = 1645.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041   5899  Z= 0.277
  Angle     :  0.671   7.878   8018  Z= 0.345
  Chirality :  0.047   0.143    927
  Planarity :  0.004   0.030   1013
  Dihedral  :  5.806  38.271    778
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.64 %
    Favored  : 89.36 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 16.18 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.73 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.83 (0.29), residues: 705
  helix: -3.42 (0.39), residues: 26
  sheet: -1.19 (0.31), residues: 284
  loop : -2.35 (0.27), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 281 
 TYR   0.015   0.002   TYR B 170 
 PHE   0.029   0.002   PHE D 247 
 TRP   0.017   0.002   TRP C 134 
 HIS   0.003   0.001   HIS B 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00665 ( 5899)
  covalent geometry    : angle       0.67109 ( 8018)
  hydrogen bonds       : bond        0.03873 (  132)
  hydrogen bonds       : angle       5.87660 (  387)

*********************** 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
  121 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 LYS cc_start: 0.8504 (tmtt) cc_final: 0.8139 (tmtt)
REVERT: A  246 HIS cc_start: 0.8161 (m90) cc_final: 0.7876 (m-70)
REVERT: B  218 TYR cc_start: 0.7356 (m-10) cc_final: 0.7098 (m-10)
REVERT: B  315 ILE cc_start: 0.9085 (mt) cc_final: 0.8791 (mt)
REVERT: C  272 MET cc_start: 0.8051 (tmm) cc_final: 0.6936 (tmm)
REVERT: D  188 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7354 (pp)
REVERT: D  243 ARG cc_start: 0.7961 (mtt-85) cc_final: 0.7606 (mtp85)
REVERT: D  282 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7771 (mt-10)
  outliers start: 21
  outliers final: 15
  residues processed: 113
  average time/residue: 0.0862
  time to fit residues: 12.3645
Evaluate side-chains
  113 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.3479 r_free = 0.3479 target = 0.123756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.105899 restraints weight = 8262.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.109357 restraints weight = 4338.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.111764 restraints weight = 2784.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.113392 restraints weight = 2003.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.114541 restraints weight = 1560.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5899  Z= 0.145
  Angle     :  0.576   7.396   8018  Z= 0.295
  Chirality :  0.044   0.139    927
  Planarity :  0.004   0.029   1013
  Dihedral  :  5.321  36.550    778
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 17.57 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.69 (0.30), residues: 705
  helix: -3.59 (0.38), residues: 32
  sheet: -1.07 (0.32), residues: 284
  loop : -2.22 (0.28), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 281 
 TYR   0.010   0.001   TYR D 319 
 PHE   0.023   0.001   PHE D 247 
 TRP   0.020   0.002   TRP C 134 
 HIS   0.002   0.001   HIS B 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 5899)
  covalent geometry    : angle       0.57583 ( 8018)
  hydrogen bonds       : bond        0.03039 (  132)
  hydrogen bonds       : angle       5.60448 (  387)

*********************** 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
  121 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ASN cc_start: 0.6146 (p0) cc_final: 0.5706 (p0)
REVERT: A  246 HIS cc_start: 0.8112 (m90) cc_final: 0.7860 (m-70)
REVERT: A  299 GLU cc_start: 0.8145 (pt0) cc_final: 0.7933 (pt0)
REVERT: B  218 TYR cc_start: 0.7343 (m-10) cc_final: 0.7087 (m-10)
REVERT: B  315 ILE cc_start: 0.9032 (mt) cc_final: 0.8739 (mt)
REVERT: D  188 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7267 (pp)
REVERT: D  277 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7885 (m-30)
  outliers start: 17
  outliers final: 11
  residues processed: 113
  average time/residue: 0.0795
  time to fit residues: 11.6176
Evaluate side-chains
  110 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
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  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 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 58 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 33 optimal weight:    0.4980
   chunk 5 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 37 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
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 = 0.3478 r_free = 0.3478 target = 0.123642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.105801 restraints weight = 8301.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.109337 restraints weight = 4360.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.111695 restraints weight = 2785.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.113324 restraints weight = 2004.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.114420 restraints weight = 1560.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.2652

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= 0.155
  Angle     :  0.581   7.588   8018  Z= 0.297
  Chirality :  0.045   0.138    927
  Planarity :  0.004   0.029   1013
  Dihedral  :  5.239  36.795    778
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.23 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.03 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.53 (0.30), residues: 705
  helix: -3.14 (0.47), residues: 26
  sheet: -1.03 (0.32), residues: 284
  loop : -2.11 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 281 
 TYR   0.011   0.001   TYR D 319 
 PHE   0.024   0.001   PHE D 247 
 TRP   0.020   0.002   TRP C 134 
 HIS   0.002   0.001   HIS B 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 5899)
  covalent geometry    : angle       0.58069 ( 8018)
  hydrogen bonds       : bond        0.03054 (  132)
  hydrogen bonds       : angle       5.52350 (  387)

*********************** 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
  122 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ASN cc_start: 0.6455 (p0) cc_final: 0.5905 (p0)
REVERT: A  149 LYS cc_start: 0.8455 (tmtt) cc_final: 0.8055 (tmtt)
REVERT: B  218 TYR cc_start: 0.7384 (m-10) cc_final: 0.7108 (m-10)
REVERT: B  315 ILE cc_start: 0.9040 (mt) cc_final: 0.8747 (mt)
REVERT: D  183 HIS cc_start: 0.6583 (OUTLIER) cc_final: 0.6309 (m-70)
REVERT: D  188 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7286 (pp)
REVERT: D  277 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7848 (m-30)
  outliers start: 20
  outliers final: 13
  residues processed: 114
  average time/residue: 0.0734
  time to fit residues: 10.9088
Evaluate side-chains
  116 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
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  280 SER
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain C residue  206 ASP
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  307 ASN
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 29 optimal weight:    0.0670
   chunk 11 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0980
   chunk 21 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 66 optimal weight:    7.9990
   overall best weight:    1.0322

-------------------------------------------------------------------------------
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 = 0.3500 r_free = 0.3500 target = 0.125490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.107571 restraints weight = 8129.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.111135 restraints weight = 4288.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.113538 restraints weight = 2735.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.115121 restraints weight = 1968.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.116270 restraints weight = 1538.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2750

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= 0.124
  Angle     :  0.563   7.000   8018  Z= 0.289
  Chirality :  0.044   0.137    927
  Planarity :  0.003   0.028   1013
  Dihedral  :  5.027  36.116    778
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 18.18 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.40 (0.30), residues: 705
  helix: -2.96 (0.51), residues: 26
  sheet: -0.94 (0.31), residues: 286
  loop : -2.04 (0.29), residues: 393

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5899)
  covalent geometry    : angle       0.56298 ( 8018)
  hydrogen bonds       : bond        0.02786 (  132)
  hydrogen bonds       : angle       5.43483 (  387)

*********************** 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
  128 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ASN cc_start: 0.6464 (p0) cc_final: 0.5918 (p0)
REVERT: A  149 LYS cc_start: 0.8437 (tmtt) cc_final: 0.8051 (tmtt)
REVERT: B  134 TRP cc_start: 0.8535 (m100) cc_final: 0.7843 (m100)
REVERT: B  218 TYR cc_start: 0.7247 (m-10) cc_final: 0.6969 (m-10)
REVERT: B  256 TYR cc_start: 0.8917 (m-80) cc_final: 0.8217 (m-80)
REVERT: B  276 ARG cc_start: 0.8253 (ttp-110) cc_final: 0.7918 (ptp90)
REVERT: B  315 ILE cc_start: 0.9020 (mt) cc_final: 0.8732 (mt)
REVERT: C  230 MET cc_start: 0.8581 (mmp) cc_final: 0.8241 (mmp)
REVERT: D  183 HIS cc_start: 0.6555 (OUTLIER) cc_final: 0.6355 (m-70)
REVERT: D  188 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7287 (pp)
REVERT: D  277 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7825 (m-30)
REVERT: D  282 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7445 (tt0)
  outliers start: 23
  outliers final: 15
  residues processed: 120
  average time/residue: 0.0853
  time to fit residues: 13.1616
Evaluate side-chains
  118 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 HIS
Chi-restraints excluded: chain A residue  267 LEU
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  212 THR
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain C residue  206 ASP
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  208 GLN
Chi-restraints excluded: chain D residue  237 VAL
Chi-restraints excluded: chain D residue  277 ASP
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 16 optimal weight:    0.3980
   chunk 32 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 249 ASN
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 = 0.3519 r_free = 0.3519 target = 0.127046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.109098 restraints weight = 8142.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.112720 restraints weight = 4260.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.115060 restraints weight = 2705.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.116740 restraints weight = 1950.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.117835 restraints weight = 1510.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5899  Z= 0.113
  Angle     :  0.553   6.588   8018  Z= 0.284
  Chirality :  0.044   0.142    927
  Planarity :  0.003   0.028   1013
  Dihedral  :  4.825  36.546    778
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 17.57 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.24 (0.30), residues: 705
  helix: -2.34 (0.67), residues: 20
  sheet: -0.84 (0.32), residues: 286
  loop : -1.97 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 281 
 TYR   0.011   0.001   TYR D 319 
 PHE   0.022   0.001   PHE D 247 
 TRP   0.021   0.002   TRP C 134 
 HIS   0.002   0.000   HIS B 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 5899)
  covalent geometry    : angle       0.55294 ( 8018)
  hydrogen bonds       : bond        0.02698 (  132)
  hydrogen bonds       : angle       5.35874 (  387)

*********************** 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
  128 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ASN cc_start: 0.6630 (p0) cc_final: 0.6009 (p0)
REVERT: A  149 LYS cc_start: 0.8431 (tmtt) cc_final: 0.8055 (tmtt)
REVERT: A  230 MET cc_start: 0.7707 (mmt) cc_final: 0.7194 (mmt)
REVERT: B  134 TRP cc_start: 0.8365 (m100) cc_final: 0.7615 (m100)
REVERT: B  218 TYR cc_start: 0.7115 (m-10) cc_final: 0.6789 (m-10)
REVERT: B  246 HIS cc_start: 0.6803 (OUTLIER) cc_final: 0.6461 (t70)
REVERT: B  256 TYR cc_start: 0.8915 (m-80) cc_final: 0.8254 (m-80)
REVERT: B  272 MET cc_start: 0.8047 (tmm) cc_final: 0.7840 (tmm)
REVERT: B  315 ILE cc_start: 0.9011 (mt) cc_final: 0.8738 (mt)
REVERT: C  230 MET cc_start: 0.8526 (mmp) cc_final: 0.8217 (mmp)
REVERT: C  272 MET cc_start: 0.7693 (tmm) cc_final: 0.7043 (tmm)
REVERT: D  188 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7277 (pp)
REVERT: D  277 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7811 (m-30)
REVERT: D  282 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7358 (tt0)
  outliers start: 23
  outliers final: 14
  residues processed: 120
  average time/residue: 0.0734
  time to fit residues: 11.5245
Evaluate side-chains
  117 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 LEU
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 B residue  280 SER
Chi-restraints excluded: chain C residue  188 ASN
Chi-restraints excluded: chain C residue  206 ASP
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  237 VAL
Chi-restraints excluded: chain D residue  274 ILE
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  307 ASN
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 64 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0050
   overall best weight:    1.4000

-------------------------------------------------------------------------------
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 = 0.3498 r_free = 0.3498 target = 0.125363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.107265 restraints weight = 8254.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.110797 restraints weight = 4358.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.113223 restraints weight = 2809.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.114865 restraints weight = 2026.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.115964 restraints weight = 1580.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5899  Z= 0.149
  Angle     :  0.581   6.808   8018  Z= 0.297
  Chirality :  0.044   0.136    927
  Planarity :  0.003   0.028   1013
  Dihedral  :  4.978  37.704    778
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.95 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.22 (0.30), residues: 705
  helix: -2.32 (0.67), residues: 20
  sheet: -0.84 (0.32), residues: 286
  loop : -1.94 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 281 
 TYR   0.012   0.001   TYR D 319 
 PHE   0.024   0.001   PHE D 247 
 TRP   0.018   0.002   TRP C 134 
 HIS   0.002   0.000   HIS B 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 5899)
  covalent geometry    : angle       0.58123 ( 8018)
  hydrogen bonds       : bond        0.02926 (  132)
  hydrogen bonds       : angle       5.37525 (  387)

********************** 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
  120 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ASN cc_start: 0.6743 (p0) cc_final: 0.6131 (p0)
REVERT: A  149 LYS cc_start: 0.8434 (tmtt) cc_final: 0.8052 (tmtt)
REVERT: A  230 MET cc_start: 0.7772 (mmt) cc_final: 0.7242 (mmt)
REVERT: A  246 HIS cc_start: 0.8125 (m90) cc_final: 0.7894 (m-70)
REVERT: B  134 TRP cc_start: 0.8525 (m100) cc_final: 0.7741 (m100)
REVERT: B  218 TYR cc_start: 0.7117 (m-10) cc_final: 0.6799 (m-10)
REVERT: B  246 HIS cc_start: 0.6810 (OUTLIER) cc_final: 0.6489 (t70)
REVERT: B  256 TYR cc_start: 0.8933 (m-80) cc_final: 0.8258 (m-80)
REVERT: B  276 ARG cc_start: 0.8210 (ttp-110) cc_final: 0.7900 (ptp90)
REVERT: B  315 ILE cc_start: 0.9029 (mt) cc_final: 0.8748 (mt)
REVERT: C  230 MET cc_start: 0.8579 (mmp) cc_final: 0.8244 (mmp)
REVERT: D  188 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7275 (pp)
REVERT: D  277 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7849 (m-30)
REVERT: D  282 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7521 (tt0)
  outliers start: 18
  outliers final: 13
  residues processed: 115
  average time/residue: 0.0741
  time to fit residues: 11.0973
Evaluate side-chains
  117 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 LEU
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 B residue  280 SER
Chi-restraints excluded: chain C residue  188 ASN
Chi-restraints excluded: chain C residue  206 ASP
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  237 VAL
Chi-restraints excluded: chain D residue  277 ASP
Chi-restraints excluded: chain D residue  307 ASN
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 40 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 42 optimal weight:    0.0370
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.6858

-------------------------------------------------------------------------------
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 = 0.3532 r_free = 0.3532 target = 0.128159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.110092 restraints weight = 8035.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.113777 restraints weight = 4211.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.116123 restraints weight = 2675.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.117832 restraints weight = 1934.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.118933 restraints weight = 1499.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   5899  Z= 0.104
  Angle     :  0.553   6.336   8018  Z= 0.283
  Chirality :  0.043   0.141    927
  Planarity :  0.003   0.027   1013
  Dihedral  :  4.752  38.517    778
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 19.26 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.08 (0.31), residues: 705
  helix: -2.02 (0.75), residues: 20
  sheet: -0.78 (0.32), residues: 286
  loop : -1.84 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 281 
 TYR   0.011   0.001   TYR D 319 
 PHE   0.021   0.001   PHE D 247 
 TRP   0.020   0.002   TRP C 134 
 HIS   0.002   0.000   HIS B 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 5899)
  covalent geometry    : angle       0.55309 ( 8018)
  hydrogen bonds       : bond        0.02626 (  132)
  hydrogen bonds       : angle       5.30174 (  387)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1004.14 seconds
wall clock time: 18 minutes 1.29 seconds (1081.29 seconds total)